I used both Beosystem 2 versions 1 and 2 with no problem with Beomedia 1 through the VGA input and allocated that to the PC button on the Beo4 remote - and I can't think why anything would be different with version 3 of Beosystem 2.
Note that this only works for the screen connected to the Beosystem 2 - not for linked TVs.