What you do works because you're replacing old files with new ones while keeping the save directory intact, which works.
But RPGMaker uses a global data file in its save folder that 'counts' how many saves were made, so hypothetically, if you were to do it the other way around, as in, creating a new folder with the new files, and trying to move the saves inside, they won't show up during selection.
An easy way to remedy that is simply to launch the game in the new folder, creating a save in every single slot, then transferring the old saves.
But it's much simpler to just copy the new files in the old folder like you do, it's just that some people feel 'icky' about doing it that way out of habit, from fear of corrupting the game if some event files create conflicts, so they tend to go the other way around.