Cassette clicking on 12-speed di2; adjustments Qs


looking for help with two issues after I got a new bike  

New bike has Ultegra Di2 so have swapped my TacxNeo 2T over to use thru axle with a 12- speed cassette (Shimano 105). The 2.7 mm spacer is on the non-drive side to clear the disc brake and the fit is still very snug.

putting the bike on the trainer there was a clicking noise occurring multiple times per pedal stroke. Suspecting alignment issues I used Di2 app to change alignment from +3 to +11 and that reduced the noise significantly for most gears. I also aligned the front derailleur while I was in there.

1) when I put the wheel back in it still runs fine and doesn’t seem to need swapping back to +3. Is this normal/ possible?

2) in the lowest gear at the back, the derailleur rubs on the magnetic disc. Is there a solution for this, should I just avoid the gear? Have I gotten the wrong cassette and that’s causing the issue?

any help or insight appreciated. Two additional details in-case useful. When I updated the rear alignment, going from +3 down to ~+1 or 0 caused the bike to downshift. The bike is a 2024 TCR Advanced Pro 0.