If the supermod's installer tells you to install the game somewhere else, you can just ignore it. It's most likely complaining because your Steam folder is inside the Program Files (x86) folder and it causes problems because the Windows UAC restricts users other than administrators from doing certain tasks in there. This can cause modding utilities to not work properly.
But you can safely ignore the warning. You can prevent problems by turning off UAC completely, or by running SH3 and any utilities as an administrator.
My Steam is installed in Program Files (x86) and all my games are in there as well. I mod them a lot using various modding utilities like JSGME or Nexus Mod Manager etc. and I've never run into any problems because I turned Windows UAC off.
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