Steam Cloud does not sync saves in the system directory (Flycast)?

It seems that Steam Cloud does not sync the system directory, which is a good thing. But, some game systems have their game save files inside the system directory, like Flycast, so my Dreamcast game save files are not synced between my machines. How can I make it so that Steam Cloud synchronizes Flycast save files ? Can I tell Retroarch to use the regular retroarch/saves directory for Flycast?

I tried to switch to “Per game VMU”, it creates a save file in the retroarch/saves directory for each game, but for some reason this save file is not synced between machines either.