Perhaps I'm misunderstanding you? What do you mean by ghost tokens?
A lot of div abilities are only good at low levels, and that's mainly as many div abilities you need either higher stats or higher HD to take or need a slew of prerequisites to take. Things like templates, force field or Perfect Body/Mind are all low level div abilities mainly made for sub epic deities of Div Rank 1-3.
One thing I do do however, is I combine Perfect Mind and Body into just "Perfect Body" and boost it from +5 to +6. Separate, it's a pretty shiit power, even at low levels.
By "ghost" tokens, I mean a kind of counter that only serves to keep track of how many wishes you have invested in the features. Let me clarify: let's say you take Perfect Mind to give you a +5 to all mental characteristics. Later, on your free days, when you know you won't need them and you can consume them without danger, you use wishes to give yourself the bonus to the mentals. These bonuses obviously don't stack but become these "ghost" tokens for that characteristic that are useless except to tell you how many wishes you have invested in that specific characteristic. When you get 5 tokens in all mentals, you lose the Divine Ability Perfect Mind and you can immediately retrain it in another Divine Ability whose prerequisites you meet while the "phantom" tokens become inherent bonuses to those characteristics because in the end you paid the price to have a bonus equivalent to Perfect Mind. So it remains a Divine Ability and no longer becomes a penalty at higher levels for throwing away a slot at low levels.
At lower level yes but already at Lesser Deity is not a good investment as a Divine Ability. The only cases in which this could remain a Divine Ability is that after you have taken it you can continue to use Wish to give you "ghost" inherent bons that do not increase your characteristic but only serve to increase this counter. When you have 5 "ghost" tokens on all characteristics of a certain type (physical or mental) that ability can be retrained immediately and without any cost because you paid to have the same benefit.
You should be able to use the Wish spells separately from the divine power without any issues. All stat points regardless of source are considered inherent after 24 hours, so if you have a belt of strength +4 for example, it's considered an enchantment bonus for the first 24 but then converts to an inherent bonus, that doesn't have any negative interaction with Wished for stat points though, all inherent bonuses stack.
You should be able to use the Wish spells separately from the divine power without any issues. All stat points regardless of source are considered inherent after 24 hours, so if you have a belt of strength +4 for example, it's considered an enchantment bonus for the first 24 but then converts to an inherent bonus, that doesn't have any negative interaction with Wished for stat points though, all inherent bonuses stack.
Belt of Giant Strength – d20PFSRD"This belt is a thick leather affair, often decorated with huge metal buckles. The belt grants the wearer an enhancement bonus to Strength of +2, +4, or +6. Treat this as a temporary ability bonus for the first 24 hours the belt is worn."
It not become an inherent bonus. It is always an enhancement bonus, simply after 24 hours is no longer temporary.
Also from wish Wish – d20PFSRD "An inherent bonus may not exceed +5 for a single ability score, and inherent bonuses to a particular ability score do not stack, so only the best one applies." inherent bonuses does not stack. The only RAW bonus that stack is the dodge bonus and eventually the natural armor gained with templates. For all others, only the higher apply.
Belt of Giant Strength – d20PFSRD"This belt is a thick leather affair, often decorated with huge metal buckles. The belt grants the wearer an enhancement bonus to Strength of +2, +4, or +6. Treat this as a temporary ability bonus for the first 24 hours the belt is worn."
It not become an inherent bonus. It is always an enhancement bonus, simply after 24 hours is no longer temporary.
Also from wish Wish – d20PFSRD "An inherent bonus may not exceed +5 for a single ability score, and inherent bonuses to a particular ability score do not stack, so only the best one applies." inherent bonuses does not stack. The only RAW bonus that stack is the dodge bonus and eventually the natural armor gained with templates. For all others, only the higher apply.
Belt of Giant Strength – d20PFSRD"This belt is a thick leather affair, often decorated with huge metal buckles. The belt grants the wearer an enhancement bonus to Strength of +2, +4, or +6. Treat this as a temporary ability bonus for the first 24 hours the belt is worn."
It not become an inherent bonus. It is always an enhancement bonus, simply after 24 hours is no longer temporary.
Also from wish Wish – d20PFSRD "An inherent bonus may not exceed +5 for a single ability score, and inherent bonuses to a particular ability score do not stack, so only the best one applies." inherent bonuses does not stack. The only RAW bonus that stack is the dodge bonus and eventually the natural armor gained with templates. For all others, only the higher apply.
"Bonuses are numerical values that are added to checks and statistical scores. Most bonuses have a type, and as a general rule, bonuses of the same type are not cumulative (do not “stack”)—only the greater bonus granted applies.
The important aspect of bonus types is that two bonuses of the same type don’t generally stack. With the exception of dodge bonuses, most circumstance bonuses, and racial bonuses, only the better bonus of a given type works. Bonuses without a type always stack, unless they are from the same source."
"A dodge bonus improves armor class (and sometimes Reflex saves) resulting from physical skill at avoiding blows and other ill effects. Dodge bonuses are usually not granted by spells or magic items. Any situation or effect (except wearing armor) that negates a character’s Dexterity bonus also negates any dodge bonuses the character may have. Dodge bonuses stack with all other bonuses to AC, even other dodge bonuses. Dodge bonuses apply against touch attacks."
Dodge and untyped specific that they stack. Inherent no.
"An inherent bonus may not exceed +5 for a single ability score, and inherent bonuses to a particular ability score do not stack, so only the best one applies."
Because of this, I consider that the general rule, not an exception of Wish. If you have a specific inherent bonus that give +10 to Strength, ok, but it does not stack with the +5 for Wish or other sourcers, only the higher apply, unless that specific inherent bonus specific that stack with other inherent bonus.
As a rule, I use that the only bonus that automatically stack is dodge or untyped unless the specific bonus specifies that he stack with others of the same type.
"Bonuses are numerical values that are added to checks and statistical scores. Most bonuses have a type, and as a general rule, bonuses of the same type are not cumulative (do not “stack”)—only the greater bonus granted applies.
The important aspect of bonus types is that two bonuses of the same type don’t generally stack. With the exception of dodge bonuses, most circumstance bonuses, and racial bonuses, only the better bonus of a given type works. Bonuses without a type always stack, unless they are from the same source."
"A dodge bonus improves armor class (and sometimes Reflex saves) resulting from physical skill at avoiding blows and other ill effects. Dodge bonuses are usually not granted by spells or magic items. Any situation or effect (except wearing armor) that negates a character’s Dexterity bonus also negates any dodge bonuses the character may have. Dodge bonuses stack with all other bonuses to AC, even other dodge bonuses. Dodge bonuses apply against touch attacks."
Dodge and untyped specific that they stack. Inherent no.
Because of this, I consider that the general rule, not an exception of Wish. If you have a specific inherent bonus that give +10 to Strength, ok, but it does not stack with the +5 for Wish or other sourcers, only the higher apply, unless that specific inherent bonus specific that stack with other inherent bonus.
As a rule, I use that the only bonus that automatically stack is dodge or untyped unless the specific bonus specifies that he stack with others of the same type.
For me it's okay to create an ability that gives an inherent bonus greater than +5 or that specifies that that bonus stacks with the wish bonus (specific rule>general rule). Inherent bonus is very unclear in both 3.5 and PF because neither WOTC nor Paizo has ever written any clear rules about it other than the skimpy line of the spell wish. I use that as a general rule but anyone is free to use another interpretation because everything is very smoky. I'd say this forum response you posted sums it up perfectly: "Agreed, the bloodline powers and items would break the +5 rule, but those are specific cases. In this case the "general rule" is given by the spell, so anything that didn't specifically say it gave a higher bonus than the general +5 would work, but if it simply said it granted an inherent bonus then the stacking rules and +5 cap would apply because the dumbass designers couldn't be bothered to properly define "inherent bonus" until the Rules Compendium for 3.5, and perhaps nowhere at all in PF"