Remap Super-key keyboard

There is a following up question.
I did remapping according to my solution.
However, I only did it in dom0 and the other VMs are not affected. I’d like to do it for all the VMs. Now my issue is that the .Xmodmap file is placed in the home directory whch however as you all know is only permanent per app. I tried creating .Xmodmap in the root directory of my template. This did not have any effect on the AppVMa.
Has anyone a good solution for my issue to change keys via xmodmap in a template so it takes effect not only in the template but on all the AppVM based on it?