Just as another data point: Booked EWR-BER on points, cash upgraded to Premium Plus (fare class changed from XN to R), unable to apply Plus Points
I did this successfully in January for HND-IAD without issue in the app. This time, there is no option to use miles or Plus Points to upgrade, only cash. Agents also refuse to apply points, saying the base ticket is an award and therefore cannot be upgraded with Plus Points
As a side note, I used ETC to pay for the Premium Plus upgrade. Agents said I could only use cash to pay for the upgrade, as did the upgrade section in the app. I was eventually able to use the credit by going through the change seat option, which then allowed other payment options, including travel credits