> How is how inputs gets routed to the right window
It is covered for both X11 and Wayland. I just don't get into the particular decisions and details of how each WM/DE picks what they deem the current focused window, since it varies widely and it's more part of window management than of input management (I've written a WM and it's a bit messy). An article on WM/Compositor development would be more appropriate for that, I have a few already on my blog.