Related: Cannot Change VM Keyboard Layout in 4.1
I can confirm a keyboard layout change not affecting keyboard layout inside qubes.
With Qubes 4.0 (If remembered correctly), I just set
setxkbmap -layout "us,nl, ...more..." -option "grp:win_space_toggle" ...
as startup script. The keyboard layout changed for dom0 + all qubes.
With Qubes 4.1 the same only changes dom0 layout, qubes unchanged. Now it is needed to manually invoke
setxkbmap <lang>
inside dom0.
Note: System Tools → Settings Manager → Keyboard → Layout → Use system defaults is enabled (default setting)