I was a Sega kid in the Genesis generation. A friend of mine got a Saturn and I so desperately wanted to like Nights because it was the thing for Saturn. I didn’t like it at all. It felt hard to control, hard to understand, and was just not pleasant for me.
Meanwhile, a different friend and I had a blast trading off playing Mario 64. Hands down, way better for a 9 year old me.
You are correct that a reboot will trigger a full rescan. I’m always on the lookout for better sync. I just don’t think it’s out there right now for easy bidirectional sync.
Basically, if you want to set and forget, Syncthing is the best option. If you want more control, you’ll need to look into setting up rsync scripts or similar, which will at least better let you control how often to sync.