I think that the primary problem is the Windows reliance upon the name of a file to express that file's metadata. I realize that this has been the way of things for decades, but there are myriad ways to differentiate file types now. Modern filesystems have improved ways of storing and reading file metadata as well, without it having to impact the system's functionality.
The interesting thing with full "regular" usage of a Windows system, it is exceedingly rare to actually deal with the actual executable file. A typical user is going to use the menu system to access the executable. I'm a computery sort of person, and I find that the only time I make use explorer is when I need to migrate files from one solution to another, or when I have to stage something for a process I'm running. On a more normal basis, I access my downloads via the browser's download dialog. I access documents via the word processor's recent documents and/or Open dialog (which opens to the established landing place for documents). I access programs via the Start Menu, or Win+Q/Win+S, or Command+Space. Steam is my primary mode of running games, too - I use the UI instead of the shortcuts for the games that are installed.
I used to use the CLI a whole lot more. I guess I just got old, but mostly, it's that sort of "I'm not going to do more work than I really have to" curmudgeon sort of mentality. When I have to navigate to an executable, for instance, HxD, I will create a menu shortcut to it instead. It's just easier. In a lot of ways, the common usage metaphors are what keep users safe, too.