for technical reasons SetApp version uses a different settings file, it is located in ~/Library/Preferences/com.hegenberg.bettertouchtool-setapp.plist
You can quit BetterTouchTool then delete the -setapp.plist and rename the old com.hegenberg.BetterTouchTool.plist in the same folder to com.hegenberg.bettertouchtool-setapp.plist
This only affects app settings, trigger setups etc. are stored in the same way for both the SetApp and Non-Setapp