I think that’s a really creative idea but I also think it’s something that I’d prefer for game specific game plans. Stopping the run is very important for a consistent defense. It puts a high floor in the defense that you make them have to throw the ball to be successful. Which, most teams can’t do very well. The goal is to win the regular season so you give yourself a shot at the playoffs and stopping the run is the most consistent way to do that for a defense. Remove the margin for error for upsets and make those undermanned teams that fill the schedule play other worldly to beat you. When the big matchups come, change it up.
I don't necessarily disagree and I do think its a risk, but I don't think you can just play one way and then switch it up in a week to face the best team you will face all year. I think you need to craft your defense (and recruit to it) based on beating the elite teams, and then figure out how to adjust it for the other teams.
For example, I think a defense built from the back would require us to recruit a lot more DB talent each year. Maybe the adjustment for our variable schedule is that instead of taking a lot of guys that can play CB and then transition to Safety, instead we take more big bodied safeties that can move down to the box against run heavy teams. Against passing teams, maybe none of the safeties could match up with a receiver, but being able to move them around and drop them into coverage could cause confusion for the offense.
Similarly, instead of linebacker basically being a size progression from Rover to Buck to Mike, maybe recruit some really solid run stuffing Mikes. If we have a bunch of athletes running around behind the linebackers, maybe they don't need to be as good in coverage, which could also present a recruiting advantage because those types might be overlooked now. In a standard defense, maybe you have one of those guys on the field, but against run heavy teams or in goal line, then you can bring some more in.