I thought the TTS Mastertuner did not leave a fingerprint a lot of people on this board posted as such.
That was true for many years, but in the past year I've questioned this on the site and got no definitive answer. I think I recommended people actually contact Mr. Cole of TTS with that question, no one has come back and posted a response as far as I can tell.
Anyone who buys a new Harley and is concerned about the factory warranty should automatically assume any powertrain modifications other than those certified by Harley as street legal will be grounds for voiding the powertrain portion of the factory warranty. The most obvious and easily detected modification is a tune, which is checked any time a dealership attaches their diagnostic equipment to the bike. Internal mods aren't as obvious, but can still be detected if you have a failure that requires disassembly for diagnosis and repair. If anyone is in a position where having to pay for a major failure out of pocket would be a big problem, they probably shouldn't modify anything more involved than perhaps a muffler. If Harley's were highly reliable and had no major ongoing issues, it wouldn't be a huge risk.
JMHO - Jerry