Every implementation I've seen pairings were hand-built (doesn't mean it couldn't be done). That's probably good, since an efficient pairing is probably good for both company and pilots. When it comes time to allocate pairings, that's where company interests and pilot interests diverge.

Global optimization means that PBS will need to disregard seniority to solve a Chinese puzzle to ensure rest/work rules don't create inefficiencies. Must have tight contractual language, otherwise your seniority will be respected only up to the point where PBS needs to give your trip to a junior in order maximize productivity.