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I Know that TL2 is not a Steamworks title, but I've noticed that some mods are only on Steam. Can these not be installed in this version of TL2?
They can. I have both Steam and GOG version and had steamworks mods installed before I got the GOG version. When I started GOG version it detected the steamworkshop mods without a hitch. Though you better check nexusmods for TL2 mods if you dont have TL2 on Steam.