They can't do this unless they are okay with never selling machines again to anyone who needs to write code. There's no feasible way for all programming tools to be distributed through MAS. IPython isn't going to suddenly go through the marathon of crap you need to get into the store.
If absolutely nothing else, native developers: you can't have more than one version of a MAS app installed. Nearly every iOS developer I know has at least two versions of Xcode at any given time.
That’s not true. Many people write code on Mac despite kernel extensions being disabled and SIP. What will be considered root will be a superficial emulation convincing enough to fool most Unix software
I doubt that Apple will completely lock down MacOS. However, for corporate machines, the presence of Apple-controlled hardware will enable more comprehensive control of the endpoint, which is arguably good for security.
Apple story on corporate support is infamously bad, and they don't appear interested in supporting buyer ownership of machines, unlike Microsoft (which requires it from the high end certifications).
They may provide sandboxes for development, some kind of WSL (Windows Subsystem for Linux) or Docker on Mac, and a "Classic" emulator for apps that haven't been recompiled like they did for the transition between Mac os 9 and Mac os X, and from PowerPC to x86.
If absolutely nothing else, native developers: you can't have more than one version of a MAS app installed. Nearly every iOS developer I know has at least two versions of Xcode at any given time.