My guess is that it is about MusicBee being consistent in its actions and trying to make data available in an as consistent as possible manner irrespective of the various existing audio formats.
(which is a to be respected effort and accomplishment by itself)
So as Bee-liever pointed out earlier, as soon as you apply volume adjustment, MusicBee performs a write action so that formats such as mp3 will store that info.
The 'Encoder' tag is another tag that is utterly inconsistent between audio (metadata) formats and encoding software.
So MusicBee will make an effort to read/update it and make it available at a save action.
Both of the above make perfect sense to me, and are very useful and sensible for most users and most user cases.
Personally it irritates me quite a bit when people that chose to use an advanced music manager that will obviously need to manage the metadata of files, and as a result might need to update files under some circumstances (without deleting or altering any of the original metadata) complain about metadata being added, or a file timestamp being changed.
I think they should look for other solutions to solve their 'problem'.