As was talked around above, the trans doesn't matter. It's the transfer case that has issues.
The model 20 transfer case doesn't have an oil pump, so the lube is only circulated by the spinning gears. With the 'case in neutral and the rear driveshaft spinning, nothing down in the lube is moving, so the rear output bearing is moving, but it's not getting lubed. That ain't good.
Back when these vehicles were new, the different manufacturers had different recommendations for flat towing (all of them using model 20 transfer cases). I don't recall who said exactly what, but some said always remove the rear driveshaft, others said you could flat tow with the rear 'shaft in if the distances and speeds were kept down (I seem to recall 200 miles and 50 mph, but I'm not positive about that). And others said you could flat tow if you put the 'case in neutral and LOCKED the front hubs.
Doing that spins the front output shaft as well, which is down in the lube. Theoretically this should work to circulate the lube to the rear output as well. I have heard from some people who do that now and they say it works for them.
Of course some people flat tow with the transfer case in neutral leaving the rear driveshaft in and front hubs unlocked, and they say that it works fine. But I've also heard of two different people (I don't recall what transfer cases they had) that fried their transfer cases by doing that. So to me it's not worth the risk.
Personally I drop the rear driveshaft. I just got back from a trip where I flat-towed my Bronco about 3000 miles. I get a little bit of front driveline vibration, and doing that at 65+ mph for 3000+ miles doesn't seem like the thing to do. And I don't want to take the risk (I have an Atlas, but they don't recommend towing with the rear driveshaft in either for the same reason). Yes, it's a bit of a pain to pull the 'shaft. But to me it's cheap insurance.
Oh, and if I'm just bringing the Bronco for a run-around-while-we're-camping vehicle I'll often leave the rear 'shaft out and run it in front wheel drive while we're at camp. That way I don't need to put it in and take it out in the middle of the trip.