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"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.