The VFT will be running off the Mandurah line. That is the proposal. Depending on timing, I prefer it to run the Thornlie line, until it hits Cockburn Central, and then run from there to Bunbury.
They'll have to build a new spur line from the Mandurah line since at Mandurah Station the line is a dead end.
If this is indeed the plan, then my worry about the Mandurah station was indeed well placed... It seems a shame that they are now coming up with this plan, rather than pre-thinking Mandurah a bit better.
It's also difficult to see where they can feed the line southward out of Mandurah... They'll most likely have to go eastward around the Peel inlet, as the area on the west is too densely developed, and tunnels are unlikely that close to water.
Since a high-speed line will have limited options for stations along the way, they may as well lay it out across low-density areas. The same goes for inter-operating with normal train traffic, thus minimum overlay with the Mandurah Line should be done.
Maybe the "inter-city express" should branch off from the Mandurah Line where the Mandurah Line leaves the Freeway reserve and continue it along the Freeway/NPBH reserve, although with construction of that already well along, this may prove difficult, as there appears little space in the median.
The other question this brings up is railcars... I'm assuming that using existing stock would be pointless, as you'll need to account for the longer travel distance by providing more comfortable seating as well as well as toilet and possibly snack facilities.
I'd like to see what sort of speeds they are proposing, too. Obviously inter-operating with the Mandurah Line will limit the train to Australind-level speeds, so it would be an improvement for that section of track. How fast are they planning to go? Rockingham should probably be avoided due to its extremely tight corner, even if the train were to stop there.