When Enlightenment is used with Wayland, the keyboard layout setting has no effect and the default layout is used instead of the configured layout.
When used with X11 instead, this problem does not occur. Also, KDE (X11 or Wayland) does not have this problem.
Tested on Arch Linux 64-bit. Enlightenment package version is 0.22.4-1
Other people have reported this as well - example here: