Manually changing your FTP is going to play hell with AT. Every time your FTP changes, your PLs will change (the current experience is this is inverse to how your FTP moves. So FTP down, PLs up; FTP up, PLs down).
At the moment if you want to use AT, you are going to have to pick which FTP you are going to use, and stick with that.
I think adjusting your FTP is going to mess with the progression levels as it thinks you’ve gotten stronger or weaker so will want to slide the progression levels accordingly (in theory if you are a 4.0 for threshold and move FTP up, you’re probably a little less than 4.0 in that category at the new FTP).
I’d guess you could consider doing each workout with the intensity slider (100% +- on bottom left) adjusted to what your perceived “bike” ftp adjustment is and maybe have better success than editing your FTP, but even this may be a problem.
The interesting question is: if you tested FTP via lactate, would you actually have two different FTPs? Or is this more of a positional limitation where your TT position is limiting your ability to produce power / recruit muscle/ breathe?