Even the 1P Voice folks are confused about this. I booked a primarily CO itinerary, with one UA segment today, using my OP number (to prioritize EUA potential). Went to assign seats, and while the CO flights were no problem for Row 21, UA wouldn't let me. Called 1P Voice, she couldn't do it, couldn't add my MP number, and said if we switched to it, made the seat assignment, then switched back, I'd lose my exit row assignment in a sweep.
Mentioned that I'd seen something here about being able to do it on a mixed itin, she got her supervisor involved who got both FF numbers entered, and now have 21 on all flights. We'll see if it sticks.
I did give her a good laugh, though, when I started the call with "Happy Customer Day 1!"