Keep in mind that the Pakenham/Cranbourne corridor is switching to in-cab signalling using CITYFLO 650 ("High-Capacity Signalling"), which coincides with the High Capacity Metro Trains.
I doubt that they will keep the old block signalling running, not only is that an added complexity to make that work nice with the new signalling, but that is an extra thing to maintain.
V/Line/Bombardier are sure to fit the latest VLocity with CITYFLO650. Probably use VLocity for Bairnsdale as well rather than bothering to fit out a Loco.
I don't know what the future holds for the Westall Train Maintenance Facility, but Comengs are being phased out, so it might not be needed for that purpose anymore.
Displacing Comengs and Siemens with HCMTs is simple enough, but there is still a small amount of other Freight services on the line (Maryvale Paper train? Westall Apex? Dandenong Cement?), which will also need to be accomodated.
The most simple solution would be to use Diesels. They can make it to Maryvale. Using the same model Diesel for all of them would simplify the integration of CITYFLO650.
Electric would get in the way of loading/unloading the containers, it is not really cleaner energy as Victoria still relies on coal power.
Trains already are the 2nd biggest user of Electricity in Victoria behind Smelting. A big heavy freight train will suck available power from the substation when the HCMT is going to be thirsty enough. Not to mention that the VIC Government picks up the tab for all Electricity use on the railway network because it's too hard to meter it, and I don't think that the Government would want to pick up the bill for their energy usage.
If they had Dual Power (Diesel-Electric + Electric Pantograph) or two separate locos (one Electric), then they have to worry about lowering and raising the Pantograph constantly, and not causing damage to the existing overhead.
There are enough Diesels on the railway network, a few more won't really matter. Not to mention it is still quite energy efficient given the amount of eight it moves compared to Trucks, etc.
Personally I think that it was dumb to procure HCMTs. Aside from supporting an evil dictatorship, they did not support the local manufacturing industry which actually still exists for building trains. It was also built for obsolete Broad Gauge & 1500V DC.
They have practically renewed the entire 1500V DC overhead and substations to make it compatible with HCMT when they could have upgraded to 25kV AC for less (Substations are smaller & pole mounted, can use existing DC overhead), and the HCMT are so delayed anyway it's not like there is going to be much coexistence.
Switching HCMT to Standard Gauge is probably not going to be practical, would require recertification, and it's already delayed enough. Plus Skyrail was built for Broad (not sure how easy it would be to convert that).
Not having Standard Gauge has really gimped the connectivity for this Inland Port (which has been planned for YEARS before Skyrail & HCMT), and limited connectivity to Gippsland.
Still I hope that this Inland Port is a raging success and justifies the building of the extra track pair on the Dandenong Corridor, but in Standard Gauge. That is realistically the only hope to convert Gippsland to SG and open up Freight out there as well.