If it ends in a situation where the resumes line up just right where Clemson and Iowa St are going to be ranked #11 and #12 with nearly equal resumes I could see it playing a role.
But it is much more likely that the situation will play out where either the Big12 team or the ACC team is clearly more deserving and will get that 2nd bid.
The leagues are close enough in strength (even though Big12 is stronger) that it just depends which league has a 2nd place team that avoided enough losses.