To me that sounds like an inexperienced CSA going about the process in the wrong way.Perhaps I should have tried to be clearer in my writing. When asking for QF291/3K779, the agent submitted it but the bot came back empty. When asking for the return trip, 3K780/QF2, the agent told outright that they can't submit partner originated requests. She offered to check if QF2, though.
For QF291, EF showed T4 but the agent told that she can submit only Y and J requests. I didn't quiz her about it but could it have been because the connection would have had only Y and J cabins?
If she was mistaken about the return trip, I'm happy to try again because that's the harder / more expensive segment for us to obtain. But effectively for now, I'm back to the drawing board to see if I can find something useful.
Usually, they will request the QF metal flights in question, then, if those requests are successful, bolt on the connecting flights from existing inventory if they are available.
I don't think MSC applies to QF->3K v.v., but it has (at least historically) on CX/AY/QF awards.