Quaduplication will still need to happen at some point to keep services moving, even with ATC, you can only physically fit X amount of trains in a given section at any given time. The biggest problem there will be land acquisition.
From what I can gather, ATC is there to reduce the length of sections, the age old principle of block working will still apply. Instead of having lineside automatic signals spaced at say 1500m apart to allow for a train that runs once per week to be able to safely come to a stand, each train will have a system on board that will let them know how far the next train is in front in real time, and then give an indication on a panel inside the train as to what speed it is safe to travel at. This will of course adjust for each train using the system, so a train like the Indian Pacific will have a larger gap between it and the next service in front than a normal suburban train would.
This system is still a fair way off, the Forrestfield line is still being signaled by conventional methods, and its going to cost quite a bit of money to be able to fit out the entire ever growing fleet of railcars to be able to work under ATC, and possibly even more to convert the PTA's nearly 200kms of track (and counting).
TransWA trains and the Indian Pacific are catered for in the working timetable, so if they are running on time, there is no delay to normal services. When the Australind comes in at Armadale of an afternoon for its run to Perth, depending on who is on the panel at Train Control, sometimes they will hold the suburban service in the dock and let the Australind out first, so it doesn't have to follow the C Pattern train to Perth. This is mainly dependant on how quick the Australind can get in and out of Armadale. Should a delay happen, then these services are simply put in where they can fit.