So, wait....PC comes to you with his character.
Character does not fit in with the campaign setting.
....This is a potential problem in almost any D&D game *not* set in Greyhawk, and isn't much fundamentally different than a PC coming to you with a gnome PC in a world where Gnomes aren't allowed, or gaining a level of sorcerer at level 3, when you only allow them to do it at level 1.
And just like in this situation, you're going to have the same kind of problems...
....would it be better for the PHB to say "Your DM has information about the races available." and then put all the races in a sidebar, because they may or may not be available? Same with a sidebar rule for not taking Sorcerer or Barbarian above 1st level?
....why do we need this when there's really just one thing we should need: Rule 0?
Letting the player know that it's different before the character creation wouldn't be too bad an option (that's why Rule 0 is the first). But if this isn't possible (just like it's not possible sometimes when the player comes to your table with a gnome, or an evil character, in a campaign you wouldn't allow it), then you're going to have to expect some disagreements.
I honestly don't see how your situation, Psion, is any different from anyone else's who has a homebrew campaign world, meeting a million similar problems. And, IMHO, that doesn't mean that the PHB should have to bother to include "consult with DM" every couple of lines...it'd be redundant and silly, because it's one of the basic assumptions: The DM can change whatever they want to.
The PC doesn't fit. Now, you have a bit of an issue -- fit the PC in (a hassle for you), or disallow the PC (a hassle for the player). Really, it's not a whole lot different. And I don't think that the book really needs to give you any more justification for it.
I guess I'm kind of confused on on why you would think this is a big issue that needs to be addressed...any homebrew is going to have these sort of problems, because it's different than the assumption -- the assumption doesn't have to be changed to accomidate any DM's possible whim...and the assumption isn't nessecarily a wrong one because it doesn't suit the campaign you play in.
It's like....congratulations, you went beyond the rules and made your own world. Tell your players what's different (at least in terms of character knowledge and generation), and let them go wild. And if you can't tell them what's different, expect a hassle when they come to the table with something that doesn't fit...
Be that a halfling in a no-halfling world, or a godless cleric in a godded world. It's the same basic issue, and I don't think either halflings or possible paths of worship need to be relegated to a sidebar when you're playing in a homebrew that doesn't match the default assumptions *anyway*, and your players should know that (or at least be prepared to either give up the character or do some hand-waving to make the character fit...'I'm not a halfling, I'm just a pygmy human!' 'I'm not a Godless cleric, I'm just a worshiper of a minor god!')