Seems like a good band-aid would be to add a free-form text field that only United software reads (perhaps in the existing human-readable notes section) that says "JOINTPNR=ABC123" that could be added by a CSR or even some kind of website tool.

If both PNRs have text indicating that they are linked, then United (and only United) would extended elite perks to the other PNR and seat the passengers together during irrops.

I'm sure it wouldn't be trivial, but it wouldn't require changing the GDS or interacting with any other airlines.