Correct. In however long I've taken transit in NYC, I have never experienced a bus driver stepping out to pee, nor had a subway train held up for that reason. I am sure it happens, and I just read up on the rules around that - but the defacto is that this causes disruptions to passengers and the system and the employees do their best to hold it in and pee at the terminus.

I am glad that the rules allow bathroom breaks when emergent but the fact that people try to minimize it tells you something as well.