The same scenario of in-state 1-A schools not playing each other, on a permanent or most every year basis, can be pointed out in Claifornia, Texas, Florida, Michigan, Ohio, Indiana, and Arkansas among perhaps a couple of others.
In California, I believe Cal-San Jose St is a frequent match-up.
Cal dropped San Jose St. about 5 years ago when Tom Holmoe became coach. He felt that there was little to be gained by beating SJS, and much to be lost with a loss. He wanted a more "national" schedule. I can see the point in this, but this does HURT SJS. Cal and Stanford could help SJS by one of them scheduling a game yearly or every other year at SJS (2 for 1). Unfortunately not the way it works. Stanford still plays SJS every year, but they play at Stanford almost every year.
This would help struggling programs though as you've stated. This would help smaller "state" programs in all the larger states.