I really don't see how some tweaks to window manager behavior to make it more accessible to Mac and Windows users are more fundamental and massive than the aforementioned change to scrollbar behavior to make it more accessible to Mac and Windows users. They were all noticeable, for sure, but from a technological perspective they were all quite minor.
Plus, I'm not sure how many of the things you mention are even changes relative to genuine NeXTSTEP rather than just differences from WindowMaker's imperfect emulation of it. Focus-follows-mouse was an X11 thing WindowMaker shoehorned into its NeXT-like environment; genuine NeXTSTEP was click-to-focus, though it could be hacked to emulate focus-follows-mouse: https://ftp.nice.ch/peanuts/GeneralData/Usenet/news/1994/_Mi...
You no longer have window-independent focus. You cannot bind hotkeys to windowing events. You cannot toggle through all windows via alt-tab, you can't set focus-follows-mouse.
Source: I've been use WindowMaker (a NeXTstep clone) for 20 years.