If you pull the drive shaft and start the engine and put it in drive, you run the risk of pumping all your ATF out on your floor, through the tail shaft housing.
I drain the master cylinder before I do a brake job with a turkey baster or a Mighty Vac, clean it out as best as possible and refill with fresh brake fluid. I NEVER push the fluid back into the master. I always open the bleeder and push the fluid into a bottle. Close the bleeders, then push the...