The problem with that theory is AA isn't listed as the owner of any the Mesa's CRJ-900s. Mesa owns 48 of their 64 CRJ-900s. The other 16 are leased, but all of them were acquired years before the AA/US merger was announced (2004-2005 timeframe) and are listed under the usual GECAS/Bombardier trustees.
Now, Mesa is under notice from AA regarding poor performance (hence losing two CRJ-900s off contract and their being used by Mesa as spares now in all white colors), but if AA owned the planes they would have ended up elsewhere so I doubt AA controls any of the leased Mesa birds.