Have you ever tried `rsync --recursive ~/LocalFolder/. you@server:/home/you/RemoteFolder/.`?
The '/.' tells `rsync` "this directory" and combined with '--recursive' (or an option enabling '--recursive' like '--archive') you can easily (r)sync a directory with all possible filenames without worrying about "extensions".
Won't create the target directory but works nicely if it's already created.

And there's actually a text/console interface for unison (package "unison240-text" on Fedora 20) so you /can/ initiate a sync without the GUI ;)