Well, simple answer to your "can you still drop the tranny with bbk headers? or with flowtech headers?" would be "YES" I mean trans do comeout either way. just one is harder then others.
since you did not specify your question. I'm assuming its LT, and your asking Can trans come out without removing passenger side headers. ya?
with BBK LT at least, you'll need to loosen passenger side header.
Donno 'bout Flowtech.
But after doing it for several times in shor time in my car with no help (trans came in and out 4 times in 2 weeks once for me Some of you old timers remenber my ordeal 2 years ago... ), you get really good at it.
I know during that 2 weeks, first time took me about all day.
4th time, 2 weeks later, I had trans out of car sitting on milk crate in less then 2 hrs.