If anyone is still wondering about this, having both %appdata%\RenPy\{game name and GUID}\* and {game folder}\game\saves\* is a standard Ren'Py thing, not something individual developers do. It means that saves automatically carry over between versions of the same game despite the game folder often changing name to reflect the new version number, but you can still transfer the game between systems without losing your saves just by copying the game folder, without having to dig into your Windows files.
The %appdata% saves let you get the advantages of all Windows' built-in features for handling individual apps' user-generated data (including automated backups) and means that game series have a standard place to find saves to import from earlier games without needing the user to show them, nor do anything else to put the saves in the "right" place.
The \game\saves saves let users who have some idea what they're doing do the things they want to with the game for the most part.
The one downside of the dual saves is that it makes manually deleting your progress a little trickier - rather than just deleting the saves from the game folder, you also need to delete the ones in %appdata% otherwise Ren'Py will just recreate the deleted version from the other (more generally, it will synchronise both versions by copying the newer version, so if you want to manually edit your save, you should only need to edit one of them).