Thanks for the suggestion Matt, but it would appear that Mamiya were indeed smarter than I gave then credit for above. I forgot to include the thickness of the paper backing in the 120 film I use! I did some measurements this afternoon.
Originally Posted by MattKing
The 120 HP5+ film plus paper is 0.14+0.1=0.24mm thick
The film channel is 0.35mm deep when the pressure plate is set to 120
The film channel is 0.25mm deep when the pressure plate is set to 220
I thought, beauty, I will just set my pressure plate to 220 when I run my film through and the emulsion will be within 0.05mm of the focal plane I tested to. nearly but not quite. I loaded a fresh roll of film, took off the lenses and poked a wooden skewer onto the film. low and behold the centre area (majority) of the film was bulging ever so slightly towards the front of the camera... I couldn't measure this accurately but my guess was about 0.1mm bulge. The edges of the film didn't bulge and were probably pressing against the pressure plate. I tried tensioning the film by advancing it as I poked, but that slight bulge persisted. This is an interesting observation because the natural curl in the film should be pressing it very flat onto the pressure plate. This bulge seemed to be the same amount irrespective of whether I set the pressure plate to 120 or 220.
Anyway these discoveries now give me reassurance that the main problem was most likely due to point 2. I made in my last post above about the non repeatability of the focusing knob's position and likely unrelated to film and perspex focal plane differences.
I will run a roll through again tomorrow with the plate set to the 120 position as it always has been.