I think it's not that difficult to strike a balance. Go with win % against top opposition once the teams have faced enough top rpi teams, set it at 8, 10, 12, or whatever seems logical. The current system is rewarding losses to top 50 rpi teams, which is plainly wrong. I have made a post about this issue in Tark seeding for D3, when a team with 4 more losses and worse record against top 50 rpi opponent (5-6 against rpi 1-50) takes the 2 seed while another team with more wins, higher rpi, and better % against top 50 rpi opponents (4-1) takes the #3 seed.
Knight D3 further illustrates that the new system is rewarding teams that simply play good opponents, regardless of wins or losses. NC Wesleyan at 27 wins, CT championship, 8-2 against rpi 1-50 gets a 3 seed while 6 S. Cal teams with worse records, losing much earlier in CT, and much worse % against top 50 rpi gets the 1 and 2 seed? That's simply illogical. The NT results, which is your proposed metric to evaluate the seeding, further shows that teams are seeded incorrectly. I can't remember any NT in which none of the #1 seeds made it past the S16.