Does the auto-installer at least give you the option of choosing the installation folder you want to use? If it doesn't that's a major design flaw. Having it doesn't impede the install-and-play user but it does unnecessarily impede the modder.
For example, my stock installation is my guaranteed clean installation. No mods. It doesn't even get played. It's only there to copy from. If I install GWX it will absolutely NOT go anywhere my stock installation. No mod ever will.
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