The easy fix is to remove the prestige caps -- and keep the prestige floors.
What Montana in Allen has done would make it a destination school regardless of its conference's success or any other factor. Right now it's a D baseline prestige. I don't see why it can't stay there, just without any cap. With its recent success, Montana should be A+ right now. If it goes 13-15 next season, I don't think a precipitous drop would be unrealistic. (North Carolina can have a losing season, I don't think Montana can.)
I've done some quick research and can't find any team in either world I'm in that's gone: E8, E8, F4, F4. Clearly that doesn't get a D baseline school to A+, would it get a C baseline school there? If so, then my simple proposal is that all schools be treated as C prestige for their upper end, and their current baseline for their lower end.