I don’t understand the confusion.
A different game (remaster) has a different save file. This is no different to having a US and UK copy of the same game - the save file is linked to that version of the game and the user ID.
As a user, I shouldn't have to care how their OS back-end operates. The OS should simply be robust enough to handle everything in such way that features simply work in a way they make most sense and are the most convenient from an usability perspective. Anything else is Lazy-devs.
Obviously this stuff is somewhat complicated in a stiff and inflexible software infrastructure, but that is just an explanation of where the problem lies, not an excuse for its continued existance.