It seems like every pci scanning solution charges by the IP. I have a server with about a dozen domains each on their own IP in order to get a certificate. Recently I have moved to windows 2012 and I know SNI is available, but have not consolidated. It seems like a racket because they scan the entire server anyway and find the same items that need to be taken care of.
I'm currently researching new scanning solutions. So far it seems like controlscan has the least expensive cost at $250 for the first and $100 for each additional.