So the biggest thing you're not considering (or at least have not mentioned) is the default schedule vs after edits. If you don't touch the conferences at all, the default schedule is railroaded to match the known games we have (I think through 2030). Eventually, though, you run out of known games and you get a random drawing of conference opponents with no consideration for rivalries. Basically, you have to control for all the variables before blaming one particular feature.
This railroading of the default schedule is what is giving the appearance of protected rivalries creating bad conference schedules. Eventually you will end up with the same bad schedules, protected rivalries or not. That's what came up when I tested this out. It is the fact that EA does not add the proper guardrails to its conference schedule generator, and the no-divisions model of large conferences takes out the few guardrails that do exist.
