NotGeoff,
the InstallGUID is used to manage some update and ini overwrite behaviors. Basically every deployment has it's own InstallGUID. If the InstallGUID of the user Revit.ini (in the user roaming profile) is different from the one in the UserDataCache Revit.ini, then the user's ini will get overwritten with the UDC version. If they are both the same then you can use the Update feature to revise (some) settings in the UDC copy, and at next launch those settings only will be revised, without overwriting the whole ini. But it only works once for each line you can update (and then not for "user" settings, which the colors are).
I have always deleted the InstallGUID from the UDC copy, so that they ALWAYS match, since the update feature is too limiting, and the overwrite "feature" is more of a bug.
The issue you may run into is that the CMD may not be able to overwrite the UDC copy when run as the user, because by default a user only has write access to Program Data folders they created. The UserDataCache folder would have been created by the user only if the deployment was also run while logged in as the user (which is not a best practice, but also pretty common). You could also have issues if a machine was originally set up for another user (so UDC was created by that user) and then handed off to a new user.
I THINK you could push the UDC copy to everyone some other way (admin user on a remote machine and the hidden C$ share with a machine list perhaps) and on launch the user's ini would be replaced, because any InstallGUID won't match blank. But I am not absolutely certain that would work, haven't double checked that behavior on recent versions of Revit.