Because those files actually store information that are useful to your project. For example if you want a particular PNG to be imported with mipmaps, smooth filter, or pixel-art filter, sRGB etc, or even not import it as
Texture but as
TextureArray instead, this is where the info goes. These files must then be in your project, and you should version them if you use VCS.
They get "auto-generated" to contain the default settings, but you may want to change them as well, per file. That data has to go somewhere, and should not be forgotten about.
The idea behind https://github.com/godotengine/godot/issues/24177 is NOT to get rid of these files, only to not put them next to project files if you did not change any default values. However it creates new issues and you will still have some
.import files next to customized resources so it's not yet decided if that's a good idea or not.
.import folder, on the other hand, is auto generated but only contains calculated data. It acts like a resource cache so the editor doesn't have to re-import everything each time you open it. It's fine to delete it and not version it, because the editor can regenerate it with no more info than what can be found in the project.