I like the idea of using IDY, CY or any other commercial yeast culture as an experimental and control for a preliminary study like this one. I think the next stage would be to test sourdough culture like Craig is suggesting, however, I think it is important to have some sort of a baseline to compare your future result too.
If you wanted to ensure contamination from flour is not a contributing factor, I would think that the participating experimenters could heat some water–using one of the dough temp formulas posted on this forum– to 130F or above (where it is known to kill off sourdough microbes), add the heated water to the the flour, let it sit for 30 mins or more, like a standard autolyse, and then add in the yeast or culture once it has cooled to room temp. Hopefully, this would minimize any contamination from the flour and not interfere with the proteins in the flour at these low temps.
At this stage, I do not think it is important to worry microbe variety as none of us, myself included, are able to isolate changes in the flora at this time, only changes in taste and performance. If we do consistently find some differences, I can contact some folks in the biology or food science depts to look into the mater. Other than that, I think it sounds like a solid plan.
BTW, what you're outlining for what you are wanted to do and how you are justifying it is very scientific for an unscientific experiment