What's the error you're getting? Screenshot if possible?
I know why this error occurs (it thinks you're playing the Steam version), but I don't know why you're getting this error. I tried a clean new game on the Itch version right now, and it does not show up for me (because it correctly identifies I'm playing on Itch, not Steam). I double checked; the error that causes this is turned off for the Itch version.
Please start a new game on the Itch version, do not try to transfer save files from one platform to another. If that does not work, reinstall the game and start a new game.