When the Melbourne Metro proposal was first mooted, the Eastern end of the project was to be at Caulfield. Nowadays it is South Yarra. Since South Yarra is simply a point where a pair of lines from Sandringham joins the rail reservation and runs parallel to the existing quadruple line from Caulfield, no congestion is experienced there. It seems silly to me that there should be a need to remove any trains from the resultant sextuple line and make them run through a separate tunnel Up of there. A portal at Caulfield makes much more sense to me.
Consider a scenario where the Caulfield to Dandenong section is eventually quadruplicated. Would it not make more sense to have a situation where, instead of two local and two express lines along that corridor, one pair (the existing pair) caters for the Pakenham and Gippsland V-Line and freight services and the new pair caters for Cranbourne services? Then, the Cranbourne lines would enter the new Metro tunnel just Down of Caulfield, making way and leaving room for the Frankston line at ground level as it exists now? Passengers could transfer between Metro and existing services and vice versa via new underground platforms at Caulfield.
Some people consider that a quadruplication project between Caulfield and Dandenong should only cater for local and express services on their own pair of lines, but if every second Metro train was removed from the existing pair, which would occur under the scenario above, many paths would be freed up on the existing pair. This should enable an increased frequency of Pakenham services and less hindrance for V-Line services at the same time.