If something works well why make major changes? It wasn't all that original at the time anyway considering the Apple Menu came along a full decade earlier. In his sketch it even appears he originally envisioned it being at the top of the screen and dropping down.
Correct, allowing programs to just change defaults themselves is terrible security. This used to be a huge annoyance back in the early days of Windows. You could install a photo viewer for example and without even asking permission it would change all of your file associations, and some programs would change the defaults every time you ran them. Then there is malware of course. User programs should never have the ability to change system settings.
Seems like people are not paying very much attention when they install Windows 10. During setup you get a screen titled "New apps for the new Windows". At the bottom of this screen is a link that says "Let me choose my default apps". If you don't want Edge, Photos or Music to be the default just click the link and uncheck them. That being said the screen does need improving. You should not have to click the little link (which sometimes you can't even see if you don't scroll down) to set the defaults. The checkboxes should be on the screen to begin with. Maybe they thought that would be too complicated and scare novice users, but more likely they know most people just click Next without reading.