I am not a KiCad developer, but I thing this whole issue has nothing to do with KiCad. Until recently I used Debian Buster with Mate (or was it Cinnamon) as desktop and I could zoom in or out of a schematic by hovering the mouse over it and scrolling with the scroll wheel without changing focus to the the window that was zoomed in or out. With my new desktop (Linux Mint with XFCE) when I rotate the scrollwheel above a window it automatically gets focus. I can even adjust my OS in such a way that focus is changed to a window by just moving the mouse cursor over it.
With my new Mint desktop focus for popup windows also behave differently when I try to make screenshots, from for example a file save popup dialog. When I press the [Print Screen] button the screen grabber program pops up, where I can select how and which part of the screen to grab. Then when I have selected that, the main program, and not the popup window gets the focus. which is slightly annoying.
Overall. Who gets focus when is a function of the OS, and I have not seen KiCad do sneaky things with it.
On different Linux distro’s and more: Desktop window managers there are all kind of ways to influence the focus behaviour of windows, and none of these have actually anything to do with the programs that are running. Whether KiCad, Libreoffice, Gimp, FreeCAD or whatever. It is the windows manager that handles it.
@BobZ: Do you see any difference in which KiCad windows are handled compared with other programs on your PC?