When a Pac-4 champ gets more points in the matrix than a BIG runner-up, there's an issue.
The easy fix is using allocations. Say the Big 12 has 8 allocations at a weight, the EIWA 3 at the same weight. Simply use Allocations minus placement. Third place at Big 12 scores more than the runner-up at EIWA.
If you want to reward Champs, instead of giving them a -1, give them a +1
In the example above, the EIWA champ gets 4 in the conference placement matrix, the runner up 1, third 0. The Big 12 champ 9, runner-up 6, third 5, fourth 4, fifth 3 and so on so that each person who earns the final allocation get the same number across all conferences. Wild Cards all lose the placement matrix automatically.