It just means a normal installation of RTW and/or BI and/or Alexander...

Making a second copy provides either a backup and/or a version on which to mess around or install mods that are not modfoldered. Some mods may pull files from the vanilla so it is important to keep it clean.

Personally I no longer use a copy because I will only play mods that are fully modfoldered such as EB, FATW, EOD, etc.

But if you want to be safe and feel you might do something silly, then do make a backup ;)