I've been noticing this issue ever since I started using MusicBee where adjusting the volume of a track would update its date modified value. I didn't know how or why, since the audio data remained the same.
I just now realized that the reason for this change in date is because MusicBee forcibly write an ENCODER tag (in this case with a value of "reference libFLAC 1.2.1 20070917") any time you save the properties of a file.
I don't want it to save or modify any tags if I don't tell it to save or modify any tags.
Doing the above will replicate this behaviour: open a track's properties, then adjust its volume before hitting save.
Below are my settings for Tags (2):