Let me state I agree it should work seamlessly. But then in today's world there are a lot of things that are supposed to work without "tweaking the system".

I will suggest that if the TA is any good you will have the PNR for each individual airline. One of the things that has improved over the last year or two is the "manage my booking" function within the OW airlines. Logon on to the airline site and you should be able to request whatever the airline itself will support. No inter-airline communications. No translation by the TA.

Mrs WF has a QF ticket ex HKG issued by an Ozzie TA. On the PNR is a joint BA/QF (same record locator) ticket and an AA ticket (handles the AA/BA potential mis-connect east bound TATL). The whole thing was issued via Sabre and all segments show up on all the airlines reservation systems. The only way I could assign seats on the AA flights was to log on to AA. (Note: BA still want $$ for advance seat selection:td:) Fortunately we are not at the point where other special requests are necessary.

My take: Yes it should work, but you can take are of it yourself if you are really that concerned.

Happy wandering

Fred