I've always done the FTP test sitting up--there is about a 15-20-watt difference in the power I can hold for 20 minutes between aero and not aero. But both are above what I can hold for most races, aero or not. I do most of my training up to about HIM race intensity in aero; for harder stuff, especially big gear work, I sit up unless the workout specifies aero.
I've asked my coach about this and she doesn't seem to think it actually makes much difference, as long as you do enough time in aero to get your body used to the position. I don't have any problem holding aero for at least three hours on the road and can push the appropriate % of FTP (tested out of aero) for the distances I do while racing in aero; it just feels awkward on the trainer. Maybe something about my bike position.