interesting reasoning!
I'm pretty sure #syncthing will be able to satisfy your requirements. I'm probably less advanced than you are, but I managed to have my home folder shared between 2 systems, with some .config files excluded.
Maybe something else to consider: make hardlinks for some config files to have them present in a specific folder, and sync that folder? This way, you sync the folder and the hardlinks on each system take care of actually using those config files, if you see what I mean?