The only way to get away with whipsawing would be to do ALL of a company's (or holding company's) flying on ONE seniority list.
If the majors had not "discarded" turboprop flying as "below them" when it started, there would be no need for scope protection today.
It is not gospel that an RJ captain MUST earn more than a 747 copilot. There is a european airline that has "regional" captains and "longhaul" copilots at (about) the same pay rate, so it's a matter of choice if you prefer long sectors as SIC or short ones as PIC.
The difficult thing is how to change from the present system to a One-List system. Pilots who have flown for the subsidiary for a long time might find it hard to accept that they'll join the tail end of the major's seniority list, while major's pilots find it unacceptable to have anyone jump ahead of them. On the long run even the former should leave regional pilots better off than never merging lists.
If the lists are merged by date, will be able to bid for all positions, so better paid regional PIC positions (if existing) would be open to mainline copilots. If the lists are just joined back to front regional pilots would obviously have to keep their positions (or at least pay).
The mainline's ability to hire more experienced pilots from the military or somewhere else rather than having to take pilots from the subsidiary should not be a factor. Seniority, after all, is designed to give the jobs to the people already with the company, provided they have the required level of experience. Better than required experience isn't really an issue. If we want to protect the airline's right to hire the "best man for the job" rather than "the most senior man able to to the job" we'd have to abolish seniority.
As I don't know of any reliable way to measure if one pilot is better than the other, we should stick to seniority, even if it stings sometimes.....
Writing from a European Regional where this might be an issue in the future.
BTW, keep the Railway Labor Act and the NMB.