I upgraded to World Traveller Plus and I believe AY is still giving only 100% for that. I got points based on AY flight number, Value level and Platinum bonus so cannot complain.

The BA side was showing that my fare class was upgraded so if I wouldn't have chickened out and would have paid for Business upgrade then I would assume that AY would have seen it is a true Business class flight.

Edit: Correction, AY web site is reporting Value (K) still so AY doesn't see the higher fare class apparently what BA is seeing. Funny thing was that once they processed the upgrade, they temporarily lost my AY Plus number from the reservation. Easy fix but maybe something to be careful at and possibly also indicating why AY doesn't see the higher fare class because it might be that BA works only within their systems and doesn't touch the Amadeus on this. In similar fashion, MyFlights app was reporting my old seat all the time and didn't show the new seat so Amadeus booking was not updated but only BA reservation side. While the World Traveller Plus produced W for me, then there is no difference from AY side as AY W wouldn't produce higher points but I wonder what happens if I would have gone for Business upgrade.