USAPA filed to become the exclusive bargaining agent for all LCC pilots and they won. Unless and until a new election is held, LCC pilots have no other choice but to have USAPA represent them. That gives the union an affirmative duty to fairly represent the interests of all pilots.
Unions have been given wide latitude by courts to negotiate their contracts. Captains make more than First Officers, pilots with more years of service get more vacation, and so on. These benefits are unequal amongst the members, but all members have the same route to obtain these higher benefits through seniority, therefore they don't violate the DFR.
Seniority is a much tougher matter. Seniority does live in the contract but you rarely ever see seniority lists changed by the union. Necessarily, if I move up a number at least one pilot then moves down a number, it is a zero sum game. If a union starts getting into picking out a group of winners and losers in seniority rights they are on very shaky ground. In this case, it is quite clear that the majority wants to take away seniority rights from the minority, rights they obtained through a mutually agreed process (ALPA merger policy). Why do they want to do that? Because they have the votes. That is not a legitimate union objective and that is a violation of the duty of fair representation.
If majority rule were the norm in these issues, what would stop a continual shuffling of the seniority list as one group cobbles together a 51% majority and agree to put the other 49% at the bottom of the list? This could continue ad infintem without the checks of a duty of fair representation.
Think back on any ruling body, city council, Congress, whatever. They cannot take away rights from the minority just because they have the votes. That is what the Supreme Court is all about, protecting minority rights. In union matters, the duty of fair representation is the check and balance against the majority pushing around the minority.
USAPA could have filed to only represent the East pilots. In that case, they could do whatever was in their power to only represent the East pilots interests. When they filed to represent ALL the pilots, they forfeited the right to disregard the interests of the West pilots. Majority rules, but the majority has a definitive duty to fairly represent ALL the pilots, not just one group or another.