I am interested is there a way to permanently make musicbee not modify music files?
1. Don't check "auto-organize media files" if re-naming the files is part of what you mean by "modify".
2. Turn off all auto-tagging in Prefs/Tags (2)
3. Do not allow replay-gain tagging
4. Do not alllow permanent volume normalization
The last item is the only process that would alter the actual audio content, the rest only alter the metadata.
The playcounts are held in the MusicBeeLibrary.mbl file, along with almost everything else about your files. I don't advise you deleting that or any of the settings ini files either, just make whatever changes you want in the GUI. If you really want to "reset everything", I would suggest just starting over with a whole new MusicBee installation, preferably Portable, after uninstalling the one you don't want anymore. Make a backup of the old one first though to avoid the "Oops!" factor. Of course, a backup(s) of your actual music files should always be kept safely elsewhere, regardless of players.