Does buying the game via Steam affect patching (i.e. are the patches delivered through Steam)? Does it impact the ability to use the beta patches?
I assume you can turn that off though
If it's anything like other paradox games, you can copy and paste the directory wholesale to run it without steam.
Alternatively, turn off the automatic updates. (Right click, properties, updates, etc)
I have EU3 on Steam and never needed to duplicate the game in another dir. Just copied all files on the Steam dir and launched the game. I don't even need a backup as long as Steam has its own backup and re-install features.