There are at least a couple of us FT'ers that have been able to upgrade TATL bonus trips with points. I always have asked, and was always told that the system didn't allow upgrading booking class x.
On my trip ORD-CPH I was upgraded to Plus with Optiontown, but OT wouldn't upgrade my daughter who had booking class x.
I told my daughter that I'll try to get her an OpUp or upgrade for points, but that there wasn't good prospects for us to get to sit together. Before I could even ask at check-in if I could upgrade her, the service rep suggested that I upgrade her for points.
I was so surprised by this, that I think I said something like, "You can't do that." But the rep said that I could, so I did. And then she gave us both an OpUp to business. Nice
She wrote on the old boarding pass my EB number and upgraded for 15000 points, and asked me to sign. The points were taken out of my account total the next day, but it took 4 days for the transaction line to appear. That was a little weird.
All in all I think that this was one of the best things EB did last year.