I like the archlinux-kde-customisation . Anyway, I had this problem from as far as I can remember ...
I added to the .desktop-files of the gnome-apps GNOME as a category, but the gnome-apps still appear in my kde-menu. I don't want to do this using the kde-menu-editor since it is only for one user as far as I know, when I install gnome-programs I don't have to worry if they have GNOME as category already included. The kde-menu contains so many gnome-programs that have a good alternative in kde ...
if you don't want to show them use kmenueditor and hide them
that creates .local/ and .config/ in your home
there your changes are saved copy that to the user you want