Guess I spoke too soon.

Apparently so was the revenue manager who reviewed that flight sometime over the past few days and also found it shocking. The manager changed my fare back, took my confirmed upgrades away for the return trip, and even my upgrade request was no longer there. I spent 40 mins on the phone with delta through several tiers of support before they finally refused to reinstate it. The last agent I spoke to really wanted to do it, but her manager refused. The only "compensation" she was allowed to offer, despite this being my 4th call to request upgrades for the itinerary, was letting me purchase the upgrade back at a discounted price. She told me to email in a complaint and maybe someone else could review it and give a better answer.

I didn't get the MQM bonus for Y on the outbound flight either, though I'm not sure I would have anyways since that wasn't the fare I originally booked. I would have been upgraded to F on those flights anyways, because of how empty they were, so I didn't get anything from that other than being confirmed a few days earlier than normally on one segment (the other cleared at the one day widow).