If it’s a road bike then it could easily make up almost the entire 20% difference.
The Virtual Power curve that TrainerRoad uses is based on known figures for resistance for the specific trainer, which is why they recommend the Kurt Kinetic trainers for virtual power use as they have a very consistant resistance curve over time which doesn’t change as it heats up.
Anyway, for a roadbike trainer tyre, recommended pressure is usually between 110-140psi so having only 35psi will have a massive effect on the power output you actually have compared to what TrainerRoad is assuming you have given the virtualpower curve.
TLDR – You need to pump the tyre up and do another FTP test I’m afraid.!