This is not just STAR, I have the same problem with ONEWORLD getting boarding passes. AA can give me a JL boarding pass but JL can't give me an AA boarding pass. "Seemless" is hardly an adjective that yet applies to these alliances, even after all these years. Try pre-selecting seats on most carriers when you've booked with another partner. And why don't our tickets include the record locators for all our alliance partner flights!

As for the TT number, it never migrates to another airline's res system/PNR. You must put it into the appropriate field when completing passport and other such details. Each airline system keeps this separately. But consider yourself lucky it was AC and not another non-American airline you were flying, IIRC AC is the only foreign airline that can issue PreCheck on its own flights from US airports.