From the article:
"Trains from Geelong would run along an upgraded section of track linking the Geelong and Werribee lines that is currently used for freight. New tracks would then be built from Werribee to Newport and link up with Melbourne Metro 2."
The barely used Werribee-West Werribee junction tracks would be used and then Werribee - Newport quadded. Werribee trains as they are now stop all stations, Geelongs express Werribee - Newport. Both metro and Geelongs then converge into the MM2 tunnel stop all stations to Southern Cross (and what is definitely not in the article is where Geelongs continue on to another short terminating station like Reservoir or Northcote or just terminate at Southern Cross [of which there'd have to be more than 2 underground platforms]). Having all trains stop at Newport, Fishermans Bend 2, Fishermans Bend 1 (assuming two stations) then Southern Cross makes sense as western metro and Geelong would want/need access to Fishermans Bend and all the jobs that are planned to go there.
I presume Laverton via Altona and Williamstown continue via Newport-Spottswood-Yarraville-Seddon etc.
"The project - which would cost tens of billions of dollars - could be built in stages, with the Geelong line upgrades to Werribee built first. The ambitious Metro 2 city tunnel would be built many years from now, most likely in the 2030s."
This fits with the NDP leaked before last year's state election - MM2 is broken up into two phases (Newport-Parkville and Parkville-Merri)
Melton-Sunshine could get the same treatment that allows Ballarats to overtake (comfortably) Melton metro services and at West Werribee, the third side of the triangle is built and a 5th platform on the western side of Sunshine. Electrify the RRL tracks from Sunshine to the City.
That would enable Mernda-Werribee to actually become Mernda-Sunshine via Werribee and Melton metros to run Melton all stations to Sunshine then follow the same stopping pattern as Vlines currently do into the city.
If Mernda / Werribee get 'HCMT'd' like Pakenham/Cranbourne-Sunbury as part of MM2, one for one train replacement boosts passenger carrying capacity (it's about 20% HCMT versus Comeng etc, no?) and if peak services move to 12 TPH for Mernda in 15-20 years (it's currently max 9TPH, average 8TPH in peaks), 6TPH could go Mernda-Sunshine (via MM2/Werribee) and 6TPH could go Mernda-Werribee (via MM2). People in Tarneit/Wyndham Vale/Truganina/any new station and suburb that will get built along the RRL tracks would have a one-seat to the city choice via Werribee / MM2 (probably good value for Wyndham Vale, not so much others) or a good service to Sunshine where they can change to numerous express and stopper services to the city or to the airport / Sunbury/wherever anyone needs to go.
If Geelong goes to 4TPH off peak - split them with every second train via the fast route (Werribee) and the other via Sunshine (for airport connections). Warrnambool will probably always go via Sunshine, plus if Geelong trains via MM2 continue past SX to at least Parkville, they've got about a ~20-21 minute trip from Parkville to the airport via MM1. In peaks send all Geelongs via MM2 and people wanting to get to the airport can change at Werribee (and then Sunshine) or just stay on the train until Parkville.