I have since also done some comparison checks and can confirm the folder structure is different, but not only that, the actual files inside are also different. I'm fairly certain Taleworlds has to make specific changes for the Microsoft store before they can release the update there, which would also explain why the Microsoft Store version takes longer to get the updates than Steam/Epic/Gog.
For those curious, here's some screenshots of the files to show the differences. Something very noticable in here is that aside from a massive differences in files only existing in Steam or Microsoft store, the Microsoft store lacks a lot of executables to launch the game, which is likely because everything has to be launched through the Microsoft Store's game launcher.