NYCT is the only division out of the 3 is that is technically the city job. The pension is managed by NYCERs while OA has a privately managed pension that is similar. If you come (or go) from another city job with NYCERs, your pension time goes with you. Your OA time does not. If let’s say you want to transfer to the subway, your time served as far as NYCERs is concerned is 0.
NYCT has civil service law protections in place that OA doesn’t necessarily have to follow. While you can work out of any Brooklyn TA depot as an OA employee, that can be taken away during contract time. Also being hired under TA allows you to work in Staten Island or any of the Queens TA depots which helps if you live in Jersey, PA or deep in Long Island.
When it comes to promotional exams, you can only apply if it’s for the same division. So if the MTA has two exams in the future for dispatcher for NYCT, you can’t take them.
The union does its best to have OA in parity with TA but it’s still not the same. Getting your foot in the door under OA is great and it’s not a bad thing, just be aware of the stips you have by being one.