I think the bag should inflate the same each time- it's constrained by the circular tank, which will act as a 360 degree cuff, plus the fact you have an airtight pump acting each way should ensure a good strong evacuation/inflation each cycle.
When I was referring to trimming, I meant the ability to account for the 1% change in water density depending on temperature and mineral content. If your boat displaces say 5kg, then that amounts to just 50ml difference. Fullsize submarines incorporate separate compensating tanks to trim for different water density, these were made larger still on boats which had to operate in both salt and fresh water. Few model submariners incorporate compensating tanks in their boats, as it means making a separate ballast system, but they are out there, often on larger model subs.
Piston tanks with some form of feedback on position allow the compensating system to be built into the main system. With pump systems this is more difficult, as they tend to incorporate an exposed water surface, which is difficult to get a reliable point of feedback, so these systems tend to be open ended feedback- e.g. mark one eyeball!
With the system Ernie has here, he should run it with the bag empty when submerged, and if the boat is bit light or a bit heavy, add or subtract a small amount of weight (e.g. lead weights) to compensate.