Add a second WB master in the System part from the App (standalone VFC case)
Connect the Slave Wishbone of the System part (coming from the App) via a WB arbiter at least to the Config Flash or even to the main wishbone bus before the address decoder.
This would allow the standalone VFC-HD to be reprogrammed with another interface than VME, and to be get all the System features.
Only one WB arbiter is required and no complexity post-synthesis is added if the WB not used on the Application side.