from the App-V and SCCM Whitepaper, pg. 30 (at
http://technet.microsoft.com/en-us/appvirtualization/cc843994.aspx)
"Note: When Configuration Manager takes control of the virtual application delivery to client PCs, any virtual applications that have been previously delivered to those client PCs using delivery methods other than Configuration Manager will be removed
from the client PCs."
Also note the special remarks on Remote Desktop Servers following that.
I asume that _after_ SCCM took control over the App-V Client you might be able to use MSI bases deployment of virtual applications again, but I would not relly on this.
I am not sure if the "App-V support" on the Advertised Programs Client can be controlled on a per-site basis...
Falko