You should use and recommend OVGME
JSGME all Mods have to reside in AC folder
OVGME you can store Mods anywhere
I don't understand the default backup ?
That is what CM, JSGME and OVGME are for :)
Anyone uses default Mods should actually use the files that exist in their stock steam folder and remove them to the default Mod
That way there will not be a single overwrite ;)
Either way you should not include default files in Mods
That is where you tell people doing a manual install to backup their files first