A couple of thoughts
-- There can be only one frequent flyer account on a UA reservation at any given time, switching as you travel is possible but can lead to unpredictable results. Best to avoid.
-- If PQDs is the major objective, I would leave the UA MP account on the ticket and after the travel request credit for the non-*A flights to a different program.
-- Calculating the PQDs for this sort of mixed travel is not easily done and is buried deep in a computer algorithm the few seem to understand. UA has stated this is based on a standard industry practice and seems related to how revenue is distributed but I have never seen a clear explanation I can use. The typical advice is just to wait until it is posted. Your experience on this is common. But you will not get PQDs for the non-*A segments (even when on a 016 ticket) and, the overall ticket PQDs will be reduced as some revenue will go to the non-*A carriers.