None of what I have read so far takes into account that the air might not be in or close to the master.
Sounds to me like you have a good handle on what the issue is, and I have used a squirt bottle with a hose on it to force the fluid up to the master from the wheel cylinder end.
It works well when you are doing the bleeding by yourself.
FYI, it's ok to only fill the master half to 2/3 of the way also because it helps keep the fluid away from the cap a little better.
that's a very good point you make about the air could be elsewhere, I was assuming as I`d bled the system several times that it was where I couldn`t get at (in the cyl), maybe a big syringe full of fluid from the wheel pushing back is the way to go
