Advice: Planescape
I've been looking for a planescape game so I'll keep my eye out if you run it here...
As for your question, if I were in your shoes, I'd probably take it on a case by case basis, with the overall goal of keeping all the characters mostly balanced with each other.
I'd try to get a good idea of what interests each player about their race selection. Are they power gaming, going for a specific ability, trying to do something "cool", trying out a concept, exploring some particular rp opportunity, etc. Some of those would let you ignore some of the racial mechanics you might otherwise have "by the book".
I'd do this for the players with standard races also. This helps you figure out what bonuses to give them to balance things out with the nonstandard races.
Then I'd handle it on a case by case basis to achieve design goals and balance rather than trying to devise some general modifier in advance to apply everywhere.
In the end, each character will get a bit more than they would for whatever level you start. For the nonstandard races, it will be racial abilities. For the standard races, it could be many different things. Maybe that's an extra level or two, maybe it's a nonstandard spelllike ability, maybe a feat or two, maybe a magic item, or some combination. I'd look at the racial substitution levels for inspiration for special abilities. Maybe give them those plus the standard class abilities they replace.