There are usually two or three additional trains for football traffic for each line.. Three lines will be using tunnel (Pakenham, Cranbourne and Sunbury/Watergardens). That will not cause a huge issue IMO running them direct to Richmond (and SSS for Etihad games) especially considering the reduction in congestion. Also, the Traralgon services will also be going direct to/from SSS and heading onto same tracks as trains coming from the new tunnel. (Chances are Traralgon services will end up a lot more frequent by the time the tunnel is built).
Also, if trains are scheduled to terminate at FSS they are likely to go via Richmond anyway. There may be crossovers coming into City South, but they are likely to want to reduce congestion from terminating trains in the tunnel.
Also if there are issues between South Yarra and Richmond, you may see some Frankston line trains go thru tunnel. We don't know what kind of redundancies they are planning on building into the line.
The aim isn't to provide a better service to the MCG for the footy, its to provide a more consistent service across every line across the board, such as 10 minute Frankston trains or Clifton Hill groups running the same way around the loop. Alternating services only after footy games goes against this.
The plan is for no trains to be terminating in the city, hence the new/improved driver facilities and stabling at Watergardens, Calder Park and Sunbury so that all trains can terminate in the outer suburbs. The only reason for a train to terminate at Flinders is to stable it in the city if its not running straight back out. The Metro lines will be mostly (exclusively?) run by the new order of trains, so they may never terminate in the city .
I'd imagine very few redundancies. With the removal of the Dandenongs between Flinders and South Yarra, this means there are two tracks that can be used for dedicated V/Line services, meaning less interaction with Frankston for them. It is in the Network Development Plan that Geelong trains will eventually run through to South Yarra (probably after a seventh track is added to the viaduct) so I'd imagine they would keep that exclusiveness.