Give it a try one time. Air escapes through the holes in the bottom of the master. If you look inside during the process, the air bubbles are visible as they escape into the master. The system is closed when plugged and once all the air vents through the holes the system locks. The re-builders include plugs for that purpose and recommend that procedure. Been doing it exclusively that way with excellent results. Never had air in all the MCs I’ve changed.
I have tried it, it doesn't always work. If all the air goes back into the reservoir it's ok. But that method doesn't push fluid through all of the passages out to the ports like what happens when you're actually using the master cylinder (they're plugged remember?). Not to mention, the crappy little plastic plugs that are supplied for that purpose don't have much strength to them, the plastic threads are not all that durable. And of course some of them are made better and fit better than others. Push too hard on the piston and it can blow the stupid little plugs out of the ports and across your bench, making a big mess. Had that happen to you yet?
This video shows both methods. The second method works better, and EVERY time. Even in this video the guy doing the better method clearly isn't super familiar with it, he's pumping the piston too fast and creating bubbles in the reservoirs with the return fluid. Or maybe he's just rushing because he's doing it for a video.
Do what you like, the method of connecting the ports back into the reservoirs is the better method if you do it correctly. If you really are having problems with the master cylinder trapping air, that method guarantees you'll clear the MC if the master cylinder is good and working properly.
Really, a lot of the time you can just fill the thing up, gravity bleed it a little and just bleed the brakes, no bench bleeding necessary. But not always, and when you really need to bleed the master cylinder because you're having issues the second method in the video is the sure bet.
