In emacs -Q, disable scroll-bar-mode and evaluate:

(let ((mouse-autoselect-window t))
  (select-frame-set-input-focus (window-frame)))

The mouse pointer will now be to the right of the window frame; with
normal window managers, this doesn't matter much, except that a "resize
this window" cursor might be shown rather than the usual one, but with
tiling window managers, the cursor position may correspond to another
window, which is then raised and wrongly receives keyboard focus. This
actually happened to me.

The attached patch fixes things, by moving the mouse pointer to the last
valid x position.

diff --git a/lisp/frame.el b/lisp/frame.el
index a8c230cb7b..7b61003c9a 100644
--- a/lisp/frame.el
+++ b/lisp/frame.el
@@ -979,10 +979,11 @@ select-frame-set-input-focus
   ;; Move mouse cursor if necessary.
   (cond
    (mouse-autoselect-window
-    (let ((edges (window-inside-edges (frame-selected-window frame))))
+    (let ((edges (window-edges (frame-selected-window frame)
+                               t nil t)))
       ;; Move mouse cursor into FRAME's selected window to avoid that
       ;; Emacs mouse-autoselects another window.
-      (set-mouse-position frame (nth 2 edges) (nth 1 edges))))
+      (set-mouse-pixel-position frame (1- (nth 2 edges)) (nth 1 edges))))
    (focus-follows-mouse
     ;; Move mouse cursor into FRAME to avoid that another frame gets
     ;; selected by the window manager.