As hard as they try to be objective and check their biases at the door they won't be able to do that completely. It's likely SEC and B1G teams will still get a bit of a boost compared to B12 and ACC teams, unless you're a "big name" school like Miami.
Unfortunately, with the departure of Texas and Oklahoma there are no longer any "big name" schools in the B12. Hopefully, over the next few years BYU can establish themselves as a legitimate "big name" school, but it doesn't happen overnight, and things will always tilt in favor of the SEC and B1G.
One positive is that with the 12-team CFP Teams outside of the P2 have the opportunity to make a statement in the tournament. It's not enough for BYU to just make the tournament, they've got to make some noise once they get there.
Go Cougars!