I just wanted to post the conclusion to my saga, that started with the brilliant idea to upgrade two CX flights in February (yes, 4 months ago).

Well, I Fedex'd a letter to the executive's office, which arrived Friday. Today, I received an email from an "executive liason" who said they agreed that "R" to "U" via an upgrade should be mileage earning and manually adjusted my account to receive credit. Account and status now reflects those flights.

So despite certain aagents and lower-level SUPs saying this is CX's problem and to go pound sand, AA actually can do something about it (albit at a higher level than a regular SUP, I assume). By the phrasing of the answer, I would say this isn't a one time exception but rather what is supposed to happen for these flights.

Godspeed to any other souls on this journey.