There are plenty of schools (I'd wager most, actually) that have some sports in one conference and other sports in another. BYU fits this bill. UVU fits this bill. It isn't uncommon at all.
You could have a P12 (D1), Mtn West (D2), and WAC (D3) conferences in each and every sport. BYU could have gymnastics playing in the WAC, hoping for promotion into the mid-tier, and football in the P12.