What John is saying is correct. (Doing brakes for my kids, I can't be anything less than perfectionist-careful.) There is a small cavity in the very end of the master beyond the outlet port that sits just a bit high, even with the car level, but moreso when you have the front jacked up to get at the bleed screws comfortably.

The leaks you had using the wrong thread on the bleeder tubes (on the bench) don't present a problem. The tubes are just to return the fluid to the reservoir, otherwise you'd push a lot of fluid getting the air out of a new master, and it would be wasted and make a mess squirting everywhere.

When you bleed using a pressure bleeder, the two circuits, primary and secondary are equally pressurized and totally separate beyond the master, so there's no reason to do one before the other, save make the process routine by following a consistent procedure.