That's pretty much how most Ren'Py upgrades have worked with every other game using this engine I've played -- including this one until now.
Nope, it's not (or at least it shouldn't be) - the main Download section in each thread provides the whole thing - and replacing files causes problems quite regularly.
I always handle it this way:
Download new version - extract into my "stuff" folder (without merging anything) - quick virus check - quick check if everything's starting up - delete the old version.
Never had any issues this way.
(And you don't have to care about savegames, at least on windows, since they're stored in your user profile.)