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I know this is a couple months ago, but in case anyone else finds it. I downloaded the GOG version of Arcanum, and followed the installation instructions of WIP 6.0 (Although I renamed my files instead of deleting them) and it works just fine! I'm really enjoying my frist playthrough of this module.
Well, I just tried WIP 6.0 with the GOG Arcanum, and it crashes with a BEX error as soon as I try to walk away from the crash site in the very beginning. I've tried installing and uninstalling both Arcanum and WIP 6.0 multiple times, its definiately a WIP issue.