This is actually quite odd, because from my experience with Mp3tag, the files can be allocated additional padding without re-creation, and thus not have its date created be touched. The date modified obviously changes. But the only time the date created ever changes is when you actually REMOVE padding, not add/increase it.
To test, I did the following:
Run a batch file on a flac in a folder to remove padding:
metaflac --dont-use-padding --remove --block-type=PICTURE,PADDING *.flac
Padding reports as 0KB in Mp3tag
Date created has changed
Add a character to a tag
Padding now reports as 4KB in Mp3tag
Date created does not change
Embed artwork to the file
Padding now reports as 678KB in Mp3tag (674KB image + 4KB pre-existing padding)
Data created does not change
The date created SHOULDN'T change when padding is added to a file. ONLY when removing. Because you can't simply remove padding from a file. Once it's there, it's there for good. To remove it, you have to re-create the file without its padding. So I don't think that is the cause for what's going on here. Perhaps MusicBee is just mishandling it in this case.