Tuner savvy/tuner friendly/tuner unfriendly means little. If you have a claim that requires them to connect your car to the mothership in Germany, then your tune will be detected and your car flagged.
Tuner friendly merely means that they won't go out of their way to find a reason to deny warranty coverage. Tuner unfriendly means that they'll try to document any mods and actively look for evidence of a prior piggyback tune.
The only way to stay sane when tuning your ECU is to consider your powertrain warranty as history and be pleasantly surprised when VW does cover something.
Nobody can tell you what may, or may not, be denied unless they have the identical car, with the identical mods, going to the same service advisor at the same time (did he/she argue with their spouse that morning and are in a bad mood?) and have the identical complaint.
In short, if a repair requires them to hook up the car to the computer for authorization then they have no choice if they want to get paid.
A flag in the system (TD1/TD4) won't affect recall work - but depending on the work that needs to be done, it may result in a future flag if the car is scanned.
You won't know if your car is flagged unless you go in for warranty that gets denied because of the flag.