It's an interesting case. The MOU signed between the company, USAPA, and APA states that there will be a request to the NMB as soon as possible to certify a single transportation system. So, the APA did that a couple of weeks ago. In RLA parlance, a "single transportation system" would basically mean that one union represents all of the pilots. Since the APA is so much bigger than USAPA, it is unlikely that the NMB will call for an election, and will probably just certify the APA as the single bargaining agent. That usually takes a little while, though, so we're probably looking at another couple of months before it's done.
So, the question becomes, if the APA is representing all of the pilots, then how can USAPA represent the Airways pilots in an integration? USAPA would no longer exist as a legal bargaining agent for anyone. That's basically the way that the APA is looking at it, and it's also how Judge Silver looked at it last month when she discussed the issue in making her ruling that the America West pilots were not entitled to their own separate representatives in the SLI process.
USAPA is arguing that this violates McCaskill-Bond, but I'm not seeing how. McCaskill-Bond simply states that Section 3 & 13 of the Allegheny Mohawk Labor Protective Provisions (LPPs) have to be used to integrate seniority lists. But Section 13.B. states that the employee groups can reach a mutual agreement on a process to use, and I'd say that their MOU qualifies as that alternative process. USAPA basically agreed to allow APA to become their representative.
It will be interesting to see how it works out. But USAPA definitely has the weaker argument of the two.