Just to follow-up:

Booking flex WT booking into Y so you can upgrade to WTP with Avios:
LHR-SFO-LHR is £ 2,056.35

Booking non-flex WTP direct, forget Avios, booking class T:
LHR-SFO-LHR, £ 1,016.35, on the exact same flights....

Unless you need your ticket to be flexible, it would appear to be a complete and utter waste of money(!) (sorry) to book flex WT to upgrade when you can have book non-flex WTP for about half the price, and save your Avios for another trip (or to upgrade to CW, but that's another story)...