They count toward the campus total set for all chapters. It's not really "quota" with a colonizing chapter...they're shooting for the full total right off the bat. Generally, colonizing chapters are allowed to recruit campus total plus a set amount more (there tends to be more new member drops with colonies, so the thought is that the new groups will probably end up closer to total after the drops, and it kind of gives new chapters a bit of a "head start"). For example, the chapter I advise colonized 7 years ago. Campus total was 95 then, and we were allowed to take 105 new/affiliate members. We had a couple affiliates, and they counted toward that total...they weren't "freebie" add-ons.
Also, the colonizing team had to approve their affiliation because they made their intentions known during the recruiting week.