Vmware Fusion + Ubuntu 12.04, shortcut
I tried playing around with the keyboard settings in Fusion, in particular editing particular profiles. 

This did not change the behaviour of ⌘ in unity. I did not play around with ⌥+` as I could not replicate your Ubuntu behaviour.

The only way I found to disable the ⌘ shortcut is to install gconf-editor and remove the shortcut from within Ubuntu running the following commands:

sudo apt-get install gconf-editor
gconftool-2 --set /apps/compiz-1/plugins/unityshell/screen0/options/shortcut_overlay --type bool false