So I instrumented dwm with some debugs and found that the terminal was indeed grabbing focus with an enter notify.
So I found a workaround within GNU Emacs. Non GNU Emacs users can just look away now. (setf (alist-get 'top ediff-control-frame-parameters) 1) (setf (alist-get 'left ediff-control-frame-parameters) 856) This has been tested on a grand total of one laptop, so left may need to be tweaked. Cheers, Sean