I agree with your sentiments on many upcoming issues with the merger, but just to play devil's advocate here, I've had this happen many times on UAX. Can't think of a time when it's happened on mainline, though.

Slightly OT, but the worst experience I've had along these lines was on USX about 6 months ago... not only was elite boarding ignored; we were specifically told by the GA to ignore our seating assignments on our BPs and just board the plane "Southwest-style" (yes, the GA's exact words). This occurred because (again, this was all in the GA's words; she announced the following over the PA @ CLT, I kid you not) the flight was oversold, and she'd taken 5 or 6 VDBs from people with seat assignments, and didn't want to take the time to assign seats to the rest of the confirmed pax on the plane without seat assignments. That lead to some VERY interesting situations once on-board the completely full CRJ... I felt quite sorry for the poor FA working the flight that day.