Let me try and set out what I think the situation is:

Revenue tickets and then upgraded.
- BA metal, POUG or AUP (see the Dashboard + glossary if necessary) = upgraded tier points (and, it appears, on other FF schemes too)
- BA metal, free opup ("involuntary upgrades") = no extra TPs, just the original one, though sometimes mistakes happen if there are complications.
- Most oneworld airlines, POUG, AUP equivalents - no extra upgraded TPs, definitely the case with AA, occasional reports of some Qatar ones slipping through the net but I suspect that's due to processing errors. This is the OP's scenario. By all means apply for the TPs but you shouldn't really get them.
- JAL domestic upgrades to First: Yes, extra TPs, provided you get properly reticketed.
- Upgrading ticket to cabin above by paying the full fare difference and reticketing = extra TPs and Avios on all airlines.
- MH bidding upgrades - if successfully upgraded you get zero, even for the base fare.

Avios/redemptions then upgraded
- Any upgrades, anywhere = no Avios or TPs, barring mistakes and errors.

Revenue ticket plus UuA plus POUG and/or AUP (BA metal).
- Should get only the base revenue ticket TPs/Avios but mistakes do happen here. (To clarify, you buy WTP ticket, you accept a POUG to CW, and/or you get an AUP to First, you should get WTP Avios and TPs).

Industry, bulk and consolidation tickets + AUP (bulk tickets generally come from cheapo travel agents, they are quite rare these days and aren't normally eligible for AUP).
- No TPs or Avios at all.