Hi Jimoz1,
I realise my comment it not going to be super helpful but I have just been through a VERY similar situation. I purchase EDI->LHR->HKG->MEL all with BA flight numbers but with the last leg (HGK->MEL) being on Qantas metal. On the "Manage my booking" it says 2X23 for the BA legs but 1 X 20KG for the Qantas leg.
All I wanted to do was know what was going to happen when I check in at BA in EDI. I spoke with BA and the response was "Please call Qantas, we will allow 2 X 23 but we don't know what Qantas will allow". I could not believe this, how can they not KNOW what the allowance is given all the flights are BA and I will check in through BA. I used the "most significant carrier" and all the arguments that you said but my ticket still shows 1 X 23kg for Qantas.
Now I spoke to Qantas and they said they "should" allow the 2 X 23KG but then again, there is NOTHING actually documented around this so its a case of faith that they will actually do what they say.
So sorry i can't help but you are certainly not alone with these types of confusing allowances...