The way it works with some highly-selective colleges (and maybe others) is that your HS guidance counselor submits a form to the college stating whether or not you took the hardest level of courses offered at your HS. That helps to even things out somewhat between say private urban prep schools, and remote rural secondary schools where there are barely enough students to offer a class, much less a regular and an AP version of it.
I don’t know exactly what the form looks like from one college to the next, but it’s likely your GC will be able to relate on it that you took the hardest courses available to you given the various enrollment constraints. Your situation is very common – it’s something AO’s see all the time.