I do agree this is a kind of serious issue. There is a lot of discussion around here in a thread about more elegantly handling file and folder renames and moves.
As I understand the current solution is a rather rudimentary handling of renamed files in the same directory if and only if those changes are transmitted at more or less the same time. (So this breaks if you rename a very large file that takes more than 60 seconds (?) to scan, as syncthing may delete the old named file before it discovers the source has a new file with the same contents under a new name.
Anyway you really have to consider syncthing handles renames and moves like the old names were deleted and the new names were created and the files just happen to have the same contents.
Anyway that’s another topic.