Why exactly would dual-voltage be required ?
Just change the entire Williamstown, Werribee, Sydenham, RRL tracks to 25kv. Sure you couldn't continue past platform 15/16/? at SouthernCross station, but that's not a huge issue.
Main problem is newport railway workshops being in a 25kv area, a bit of a good and bad news thing.
Dual-voltage rollingstock is required because it is otherwise impractical to get regional EMUs or locos to the Newport workshops and elsewhere on the suburban network. Leave the Williamstown, Werribee and Sydenham lines alone - just electrify the RRL tracks and the RFR line past West Werribee at 25kV AC. Don't do any more than necessary. As I said earlier, dual-voltage working is trivial nowadays if you use the right rollingstock.
Converting the rest of the network is uneconomical and unnecessary. 1500V DC works fine for metro networks - the higher service frequencies mostly make up for the need to have extra substations along the line. If you start talking about that then you may as well go the whole hog and convert the lines to standard gauge at the same time.
If you wanted to fully recline into armchair mode, then you should build Melbourne Metro at 25kV AC and convert the Cranbourne, Pakenham, Sunbury and Melton lines to 25kV AC. Run that group of lines as a completely separate part of the network as PTV intends to in the future.