Maybe an error message could be displayed when those filesystems are detected. It took me a while to figure out why no mods would load. Symlinks are only supported for NTFS or ReFS on Windows, so Stardrop's mod linking function didn't work. I'm sure it would be possible to work around this issue somehow, but that seems like a lot of effort for such an edge case.
It should also be noted that only the AppData directory (where Stardrop tells SMAPI to load the mods from) needs to be on NTFS/ReFS, the actual mod folder location works just fine on exFAT at least. I haven't tested with FAT32.
Maybe an error message could be displayed when those filesystems are detected. It took me a while to figure out why no mods would load. Symlinks are only supported for NTFS or ReFS on Windows, so Stardrop's mod linking function didn't work. I'm sure it would be possible to work around this issue somehow, but that seems like a lot of effort for such an edge case. It should also be noted that only the AppData directory (where Stardrop tells SMAPI to load the mods from) needs to be on NTFS/ReFS, the actual mod folder location works just fine on exFAT at least. I haven't tested with FAT32.