The choice of the 'right' fonts is very situation-dependent. A font that's perfect for body copy might be terrible for headlines, and vice versa. Therefore, the selection of typefaces can not be left to the operating system, because as you rightly pointed out, it will always use the same default font. While that default font probably isn't the worst of all fonts for any situation, it is certainly not the best.

However, delivering the best experience must be our goal. Therefore, it is important that the decisions which font to use in which situation is consciously made. Using a font stack is just a good practice to ensure that users who can't load webfonts or whatever still get a font that was picked carefully to suit the situation. That way, we as designers can still deliver the best possible experience even to users who for whatever reason can't use our first font choice.