And obviously, encrypted folders can’t be accessed through the file system even with the fuse add on, because that would break the whole point of encryption.

To me, the one big advantage Seafile has is its e2e encryption and encrypted folders, as it allows me to host it externally without allowing access to my files to the server administrator.

I looked at the comparison for Seafile as that’s the one I’m most familiar with. In my opinion Seafile’s greatest strength is its encryption, but in your comparison you seem to see this as a negative as I assume this bullet refers to the encryption? “isolated on-disk file hierarchy, incompatible with other software. much worse than nextcloud in that regard”