If you run the Flexera Inventory agent directly on a Citrix server it will generate a standard h/w and s/w inventory of what it finds on the local machine, so yes - that would be no different than running the agent on any other windows server.
The purpose of the XenApp/XenDesktop collections via the beacon is to collect information about what apps/VDI's are published and available (& possibly used) to end users and groups through Citrix (as opposed to a specific inventory of the actual Citrix server).
Hope that makes sense.
- Murray
