Yeah, the enlarged ones are for RPGMaker format so the terrain tiles are arranged differently.
If you want to use the master autotiles, you'll need to enlarge them to 200%. You can do it in something like photoshop as long as "nearest neighbor" is checked. Otherwise you could use a tool that will enlarge them, my friend fmoo made some that will help: https://fmoo.itch.io/autotile-packing-tools
Good luck, thanks!