Looking through previous threads, it looks like the strong defense preference is tied to points allowed per possession. Is there a modifier to take into account the strength of the opposition? If not, it would seem to provide an incentive to not schedule strongly.

correct, no SOS modifier.

a small incentive... relative to the many large incentives you have to run easier or harder schedules. low-mid d1 teams almost have to play for wins because they have such an impact on prestige and HCA. high end teams in all divisions really really should be playing very tough schedules, as close to 100% human as possible. the defense preference thing, IMO, is dwarfed 10-fold, perhaps 100-fold, by factors like that. but i certainly agree with your logic here!