The committee could easily decide to give the #1 overall seed to UCLA, given the sheer number of ranked teams that they have had an opportunity to play and defeat. If that meant that UConn was #2 overall, I couldn't say that was unfair.
But I also don't think it is that significant. It would theoretically mean that UConn would get the #7 overall seed in the Elite Eight round instead of the #8 seed, but Elite Eight pairings are likely to be distorted by other factors (such as avoiding intraconference re-runs) that it isn't likely to make much difference. If UConn can't defeat EITHER the #7 or #8 seed in the Elite Eight, then the team doesn't deserve the National Championship.
Really, the only effect of this decision is that UConn would wear blue rather than white uniforms when/if it faces UCLA in the Championship game. Last year, wearing blue uniforms in the semifinal round, UConn beat UCLA by 30 points, so that shouldn't trouble UConn fans very much.