I'm not so sure that the issue described in that article has anything to do with the Agent's "key" in the agent database.
As a quick test of that, I cloned a VM workstation in my lab system, then started both machines (the original VM workstation, and the cloned workstation). Both agents started fine, no issues with detection, etc. I additionally ran a full Endpoint Discover scan on the machines...also, no issues. Obviously this is a very small scale test, but would suspect that if there were going to be communication issues, I would have seen them there if it was indeed something as a result of that agent key.
It appears, based on that article, that it is something specific toXenDesktop images created using XenConvert. It would be nice to know why that is, but the KB article gives very little information.
I've seen customers of mine use images for physical machines where the agent is included in the image, and don't recall ever having any issues with that, either. All of which says to me that it's not desktop images in general, rather something specific to images created using XenConvert.
~Keith