Figured I'd add a 2020 data point. I bought an economy ticket (Q) through Concur, and then immediately used the United website to buy the upgrade (via the Reservations page "upgrade flight" link - not the pop-up directly after booking on .com, because I booked through Concur).

This generated a "Receipt for Ancillary Purchase with United" email for a "Premium Cabin Upgrade" and sent a second United eTicket itinerary that reflected that I was now booked in Z, and underneath the original eTicket number was "Premium Cabin Upgrade" with a second eTicket number.

The MP accrual information in the email updated to reflect PQP based on the total cost of the ticket, but the award miles remained the same.

In my MP Activity screen, when the flight posted, it showed the normal (economy) accruals for miles and PQP. Later a second entry, "Day of departure upgrade" was added that added the additional PQP, but no additional award miles.

This was super annoying, because I would've had an additional 12,000 award miles if it'd been booked in Z the whole time (but my job doesn't let me do that). It also is inconsistent with an experience I had last year, where buying up to P/Z resulted in award miles on the entire ticket amount. But... I don't recall in that circumstance if I called in to ask them to pay up to P/Z, or if I did it on the website. I'm betting I called. Accordingly, I'll call the next time I do this and hopefully it'll result in PQP *and* award miles being based on the upgrade.

Customer service, as you can imagine, has been useless:

• called the premier line, they said to use missing miles form, did so, it was instantly rejected b/c flight was already credited
• called the premier line, they said it's never been the policy to credit award miles based on full upgraded ticket cost; I pointed out they'd done this just last year on a ticket, they said to email mileageplus
• emailed mileageplus, they said the same thing, and when I said the bit about last year, they said to call premier line
• called premier line, they yammered on and on about status qualification no matter how many times I said that was irrelevant, they eventually said to email screenshots to mileageplus
• emailed screenshots to mileageplus, they went radio silent; will update when I heard back

edit 3/7: after sending screenshots, got a nice email apologizing for the confusion and awarding the missing miles. Next time I'll try upgrading by phone instead and see if it makes a difference up front.