Claiming the Metro tunnel is required for airport rail is a complete hack cop out.
We have quad track to Sunshine already, as well as all the platforms at Southern Cross we could ever need - there's nothing preventing the airport link being built now. We should start on the other amplification needed on the network now instead of feigning surprise when western growth continues - in terms of groups we have:***Sunbury / Wyndham Vale***
Quad track should be provided beyond Sunshine to Deer Park Junction and Albion Junction to eliminate any interaction between the two track pairs currently leading to Sunshine from the city. The RRL should simply revert to a suburban line and be filled out with something on the order of eight stations between Sunshine and Werribee as the Wyndham region continues to grow. Upon completion, this would share the Metro tunnel with the Sunbury line, which could be extended northward if desired to provide further suburban growth. Providing 8-10tph to each branch would hardly be difficult.***Melton & Ballarat / Airport & Bendigo / Seymour (SG)***
The other track pair to Sunshine could provide the suburban service to Melton, with up to five intermediate stops between Sunshine and Melton (Deer Park and Ardeer served by Wyndham Vale services). Double track would be sufficient between Caroline Springs and Melton as Ballarat express services would struggle to catch up to all stops services. The rest of the line's capacity would be devoted to Airport services, extending out towards Bendigo (rejoining the existing line north of Sunbury), as well as all regional services to the northeast. Since this would be segregated from the greater suburban network, it could provide a simple means of converting the regional network to standard gauge.***Werribee & Geelong***
With only four intermediate stops between Newport and Werribee (replacing Aircraft with Derrimut Rd) there is no reason for the service to Geelong to be anything other than an extension of an all stops service to Werribee (especially considering the length of suburban services such as Pakenham and Frankston). Providing a direct connection between Southern Cross and Newport would result in a substantial decrease in journey time as well as opening up Fishermans Bend by allowing for an intermediate station.***Craigieburn / Upfield***
These could be considered paired sharing the northern loop once Footscray services leave to use the new tunnel. To serve growth beyond Craigieburn, one could either extend the current line northward to Wallan (with three intermediate stops currently planned), or alternatively run services express via Albion. Access to the airport for residents in the city's north could be provided by rerouting the Upfield line there via Campbellfield, Broadmeadows, and Gladstone Park. In any case, stick one of these routes on the viaduct and you've got two metro routes with little difficulty.
The service between Williamstown and Footscray is not sufficiently large to require anything more than a light rail service, whilst the Altona Loop is better served by buses. The capacity issues are greatly exaggerated, and even without the metro tunnel it is not difficult to provide a service on the order of 10tph to most locations - complete metrofication by isolation of each branch is not outside the realms of possibility. Providing six tracks to Sunshine may eventually be required, and could be provided for using low clearance swing bridges across the Yarra to connect the docks (including Webb Dock) to the freight rail network and reprovisioning the existing freight pair through Footscray for passenger purposes. Additionally, for rail services to be provided to the airport, additional trackwork for freight services will need to be provided between Sunshine and Jacana, but again, not an insurmountable challenge, and not something for which the metro tunnel is a prerequisite.