You can get value out of yabai even without disabling SIP to add the hooks into Dock.app. The things it needs that for isn't that long of a list, see the first bulleted list here https://github.com/koekeishiya/yabai/wiki/Disabling-System-I... , maybe you don't need those / can replicate them without yabai?
When I initially read this on that page,
> The following features of yabai require System Integrity Protection to be (partially) disabled:
, I thought that meant "so yabai just won't work at all if you don't disable SIP", but it's not the case at all. I use hammerspoon to deal with spaces, and don't care about window transparency/shadows/animation, and I don't know what "picture in picture for any window" means. I do miss stickiness and per-window floating (which are features I used in XMonad), but it's fine, I'm not going to disable SIP for those.
Particularly, if you just want focus-follows-mouse like in X Windows, yabai gives you that without disabling SIP.