My recent flight distances on AA flights match the slightly longer figures on milecalc.com (not EF).

However, AA's distance calculation may not be relevant here.

While you're crediting to AA, you are flying on CX, so CX is going to be paying AA for the EQM/EQD/RDM you earn on that flight. As such, I'd say it's likely that CX will be responsible for calculating distances and reporting that information to AA.

I'd recommending doing what JDiver suggests and booking one more short flight.