There is EM agent running on guest OS and uploading data to EM server. At EM server end we need to identify which VM guest the uploaded data should be collated to. If EM agent running on guest OS gets the UUID that is shown in VM Manager it can be used to collate the data at EM server end.
I may misunderstand what you're saying... but I have all my VM guests attached to EM and there is no issue of collating data to respective guests. What are you trying to collate? VM server performance and VM guest performance?
If so, this is why you attach the VM manager to the EM server. Not that I particularly like the results.... this is how you do it.
I have never installed the EM agent on Dom0. I always taken the approah of install in the EM agent on the guest and then attaching the VM Manager to EM. Thus, you get the performance stats of the guest themselves and the performance stats of the VM Servers themselves. I know it works. I'm doing it now. I do have collect issues from time to time and its more prevalent on some hardware than it is others.