Couple things (from a fat guy whose probably R&R'd more 02Js in A4 cars than a lot of people will ever even see):
I've never once, ever, taken a flange off of the transmission. You totally do not need to do that. You can even leave the unbolted axles hang there if you want.
You can R&R it with the subframe in place, the trick is (and this is a method right out of Volkswagen's own service lit) to use the spare tire jack to move the engine/trans forward, away from the subframe for more clearance.
HOWEVER, because I'm getting older, and beating the clock isn't as much of a concern as it once was, and I don't have the help I used to have, AND I often find the need to do some other things while in there, I've taken to dropping the subframe out anyway. Here's why, and here's how:
Clearance is why, it is a lot easier because you do not have to do the twist/roll/turn/flip method to R&R the box, you can just slide it right off and I can use the transmission jack then (so I can do it by myself, with no worries of anything falling). You also don't run the risk of stressing any 20+ year old hose or bit of plastic because you don't have to move the engine as much.
I leave the steering gear in the car... the four bolts that secure it to the subframe are easily accessed from below, and I can flip the power steering pressure line up and over the top of the transmission when I take it out, so it stays attached to the rack and the pump the whole time, and there is no fighting it at all. You can then do anything with the control arm compliance bushings, sway bar links and bushings, etc. easily while it is out and apart.
It only adds about 10 to 15 minutes of time to R&R the subframe, and it makes the actual transmission R&R probably at least 5 minutes less work, and again I can do it by myself. I used to wrestle them out by myself doing the twist/roll/turn/flip, but the time it takes my body to recover and the fact that my grip isn't what it used to be means I would have another tech help me... but those guys are all gone now, the only one that has the ability to help smells like a rancid ash tray and I don't want to have to stand that close to him.