That's really only true if your mental model is saving the state of the project or program. Most people want to save the state of the image, and exporting layer, guide, and other data is secondary to that.
To put it another way, all the data you want "Save" to save isn't actually important to most people who want to use the "Save" button, and if it is they're most certainly aware of which image formats preserve that information.
Having three different ways to save something depending on what you want to preserve is an odd way to do things that I'm bitten by every time I use GIMP.
