other than adding cover art, if that option is selected, does eJukebox make any physical changes to the id3 v1 and/or v2 tags and if so, is there a way to prevent it from altering the tags?

eJukebox saves the popularity counts and your star ratings in the id3 tags, plus the cover images and the text tags you edit with the editor.

You can prevent eJukebox from altering the tags if you put all your mp3s on a network drive. You set this network drive as "read only", then you build your eJukebox database from this network drive. So eJukebox can only read your music..