The rest of your post is all correct, but there's nothing unique about different pricing on interline/codeshare flights from different airlines.

I once bought a ticket from UA that was AC YYC-NRT, NH NRT-SIN, UA SIN-SFO, AC SFO-YYC, all in J. AC's website wouldn't sell it to me. When I phoned AC, I think it was over $10K. UA sold it to me, all online and super easy, for $4K.

I could cite a bunch of other examples, even of pricing differing between selecting the codeshare vs the native flight number, ticketed by the same airline, due to different inventory (e.g. codeshare is P0 but operating carrier is P1).

Hard to say whether OP's experience is being caused by the AC/QR inventory oddity or just the usual interline/codeshare nonsense.