> if i _truly_ own my computer, then this could never happen.
Sure it could. You can own your house but choose to rent your furniture or borrow a couch from a friend. You then no longer have total control over those pieces of furniture, even if you do own your house.
Similarly, you can control your computer but choose to run specific software on it that automatically updates and changes itself. You can also choose not to do so. You are fully capably of not running Edge or IE, and choosing an old static version of Firefox with automatic updates disabled or some other browser that doesn't automatically update.
By choosing to install and/or use those applications that update automatically, you are opting in to their behavior. It was not forced on you. That goes for browsers, but it also goes for Windows. I don't think it makes sense to say you don't control your computer because of choices you made about what you run on it, especially when you still have the ability to change those choices.
> a user must have already installed this application manually.
All the major browsers switched to shipping Flash with their runtimes years ago so they could control the update process and make sure it was patched. Flash is shipped with Firefox, Chrome, Edge and IE (the latter two with OS updates most likely).
> this is more akin to microsoft shipping an update that removes VLC, and hence from the 1st of january, all your mkv videos stop playing.
No, I think you misunderstand what's going on. From the article itself: "It is worth noting that this change won’t affect your browsers where Flash will still remain a built-in component until the next big browser update." That next major browser update is when those browsers, Chrome and Firefox, are also removing flash. Everyone is doing it now because a year or so ago Adobe announced all support for Flash was ending at the end of 2020, and none of them want to ship an unsupported component with a bad security history.