Flatpak updates work pretty much the same way. The new version is installed into a parallel directory and takes effect the next time the application is restarted.
So I'm not nuts. My work laptop recently changed from Fedora using flatpak to Ubuntu using snap and with flatpak, I'd get a couple notifications "Hey, XYZ was updated" and on the next reboot, it was new. With snap, I have to shutdown the application, update it in a console and relaunch it. Meh.