Then it would probably work with mods in win32/Windata. But instead of moving the mods there, I would use the x64 version and start the game with win64/Application-x64.exe. I guess your icon on desktop or in start menu is connected to win32 and that should be changed or you create a new icon to start Banished.
It seems to be a specific thing in GOG installations with separate folders. In Steam installation are both exe files in one folder using the same windata. I hope its helping and not just more confusing. :)