I mentioned this in the Steam forum but I'll repeat it here.
You put the user configuration stuff for VE in the ~/Documents folder where it really doesn't belong. OSX has ~/Library/Application Support as the place for applications to store ancillary configuration and such like.
You could make a case for save games going in Documents but it's pretty atypical since these are not files a user is meant to interact with or use outside of the game.
It's not mandated but good practice to follow the customs and idioms of the host platform.
Best,
Matt
On the windows platform it is the same, if not worse (i mean generally, not VE-specific).
Configuration files, saved games, screenshots, etc. often end up in folders you do not even
have access to. (thank you very much windows 7 >:( ) And with steam-games it can get worse even.