The problem I see with your theory is that firstly brake fluid has a very low expansion rate due to its molecular makeup and also the reservoir is large enough to cope with any expansion and secondly air bubbles will always get to the top eventually, so the air will always end up in the master.
There arent many places for air to get trapped apart from the cross over tube on a stock system , there are a few nooks in the calipers but nothing that a good ride wouldnt solve .
One thing I dont condone is pressure bleeding and it is bad practice in my industry, this causes a lot of air compression and when released the bubbles tend to divide whilst trying to escape under pressure , its okay to start a bleed, but you must do a proper bleed after to release the remaining bubbles.
This is why I am not particularly keen on vacuum bleeding as the initial rush of fluid breaks up the larger bubbles into froth, I am sure you have seen this when you crack the bleeder under vacuum.
As for the bite being at different intervals with different thickness pads , I would expect it to be the same initially but different as the pads heated up.
Its a bit of a black art really and there are so many variables to consider, its not very often a true source is found for braking anomolies apart from the obvious mechanical attributes ,it could be line diameter, heat , pad material , master cylinder size and many other things including the cap on the reservoir.