Yeah - I think that it makes sense, but these vCenters within vCenters always made my head hurt.
Let's try some quick graphics. Is this a (very) rough approximation of your environment?
Graphic Assumptions: There is a Virtual Machine which acts like a "mini" vCenter, but controls *just* VDI Desktops (regardless of the ESX host on which they reside)?
If this is the configuration, are you seeing all of the VM's - meaning, can you see those outside the VDI "box" and those within?
"Please excuse the crudity of this model. I didn't have time to build it to scale or paint it."