I have a bug when calling ediff3, the layout is not a balanced.

Ultimately I found that combining this settings were the culprit :

(setq window-combination-resize t
      even-window-sizes nil)

;; you can test it with eg :
(setq default-directory "/home/user")
(ediff3 ".bashrc"
        ".bash_history"
        ".bash_logout")

Removing the manual resizing when splitting windows and relying rather
on 'window-combinaison-resize' to balance the layout, solve the issue.