Speaking as both a user and developer with experience on this topic... Not quite sure what you're saying, here. Of course the saves have to be synchronized. But it's not a manual process. What you, as a user, have to watch out for, is having both instances running at the same time, or starting/ending without internet access. The Steam cloud save by default synchronizes when you start and end the game (it just loads save files from the cloud when you start, saves them to the cloud when you end). It is entirely possible for a developer to make it much more real-time, but this requires having the game itself hook into the Steam API and either trigger the process manually or send data directly through the API, which is kind of a pain in the ass, so developers rarely do it. (Steam objects to being played by the same account on multiple devices at the same time, anyway, but if you leave a game running and it goes to sleep/hibernation, the save file won't have been uploaded.)
If you have connection always on and stop the game on one platform before starting it on another, the cloud save should "just work" with no more input from the user and very little work on the part of the developer (just need to tell Steam what save file(s) to vacuum up).
One other thing to worry about is old saves. Steam allocates a pretty small amount of cloud space for save files and tends to delete old ones. If you're shelving a game for a while, maybe keep a local copy around with your latest save file if you don't want to lose it.
Yeah, I was thinking of save states a la emulators, if that helps clarify things, but it's purely from a non-coders perspective, and is probably completely pie-in-the-sky.