USA Today/More Disturbing News for US Airways

Do our wholly owned express carriers report their own numbers to the DOT?
Each certificated carrier that is required to reports their own statistics to the DOT. Since PSA & PDT are certificated on their own, they would report their own statictics (MDA operates on the mainline certificate so is included in mainline for the DOT stats). However, only carriers that have at least 1% of domestic passenger revenues must report statistics to the DOT. PDT & PSA don't come close to making that threshold, and thus don't have to report.

Do our contract carriers each report their own numbers?
No, for the same reason as above. Mesa (the complete Mesa, not just the US portion) is probably the closest to having to report as they'll probably pass $1 Billion in revenues this year (if they didn't last year).

Could part of the reason the mainline numbers are so high be from miscoded bag claims?
I have no idea how US apportions missing bag claims to the various carriers, other than when the figures were in US Daily the Express operation as a whole had higher PAWOB numbers than mainline (often double or more). However, here's what 14 CFR Part 234 says:

"Each reporting carrier shall report monthly to the Department on a domestic system basis, excluding charter flights, the total number of passengers enplaned systemwide, and the total number of mishandled-baggage reports filed with the carrier."

Jim