incidentally, an icon fence app used to exist for windows, but i think it wouldn't have applied to newly created shortcuts anyway.
but, maybe it's possible to write a script that will move every newly created shortcut xxxx pixels to the right? not an elegant solution for sure.
window managers that can treat dual monitor setups in a versatile way exist. but they don't support icons.
maybe it is possible to tell the icon-generating software, a.k.a. desktop manager, which is the file manager on mate iirc, i.e. caja - well, maybe it is possible to tell caja to completely disregard the left monitor?
maybe you can use mate wih a different window manager that allows more fingrained control?
maybe you can set up 2 X sessions - one only for the vm, the other for "normal" stuff, each being assigned one monitor?
maybe you can seperate the monitors in a way that does not just extend the desktop size? (xrandr documentation)
no definite advice, sorry, just thoughts - ideas.
ultimitaly i guess what i'm trying to say is that mate isn't the best environment for this sort of endeavor.
and who needs desktop icons anyway