I (used to) work in academic IT and I hate articles like this. People would assume there is a serious problem, turn off a bunch of services, run a bunch of random-ass shell scripts, and then forget that they'd done all that and at some random point in the future discover that some feature wasn't working, and blame me.
I swear I really wish there were a way to output an entire OS's "diff" from default settings. Every preference pane, every terminal setting, every changed system file. So that you could both discover, in cases like this, what's changed -- but also simply so you could export your settings in a space-efficient way and (selectively) re-import on a new OS install.
(The main or second main thing now would be window management, the period I was using both made me like i3 now sway more and more, and grow to find macOS even with yabai or similar much more difficult and messy to use.)