We may be at cross purposes here. I thought you meant the original restriction that you can't MFU tickets which have non-BA sectors in (like the OP's does) even if award space is there. That did indeed go away a while ago - the OP did mention clicking upgrade with Avios so I assumed that was the issue at hand (if there is award space there, he should be able to upgrade with Avios basically).

I see the OP also mentioned clicking through for upgrading for cash. And there's two scenarios there to complicate it. If the original ticket rules permit, you can call up and pay a fare difference to a higher cabin. The cost wil be whatever the change fee is + fare difference + any increased taxes. That also seems flaky online so calling is the answer.

What you've mentioned sounds like the POU offer. My understanding is that this "deal" is indeed still not offered on flights with connections so in your specific case the agent is right (but I'll defer to someone who flies from the regions more than me as that may have changed recently).

There are so many wrinkles with the various forms of upgrade to think about!