I think the 3 car running on the Lilydale/Belgrave line has something to do with Alamein shuttles which have to terminate in the up siding at Camberwell, which can only fit 3 carriages, the trains are probably split regardless of whether they can even make it to Camberwell. Ditch the Alamein shuttles and the accompanying siding (make it four tracks Burnley-Camberwell already) and the entire Burnley group would be 6 cars.
It used to be even worse though, in ye olde days (up to the early 2000s) they used to lock the rear cars after dark and have only one carriage in use. Occasionally the driver would forget to swap the "active" carriage to the front at the end of the line and everyone would end up in the last carriage instead. On the rare occasion people would sometimes get on the train without the driver seeing and then get stuck inside when the lights went out and the doors closed, having to force the doors to get out or press the emergency button if the train was one of the few refurbished ones at the time (the doors between the cars were also locked back then so you couldn't simply walk through). The one carriage operation happened even if a Hitachi was running the service (even back then they were forced to stay as 6 cars) - five cars would be locked and in complete darkness and it would be a long walk back to the station exit if it wasn't at the front of the train.
I remember one night in the late 90s we had a defective (and cancelled) up Lilydale train (a 3 car Comeng), which sped past us whilst waiting at Mooroolbark at around 9 or 10PM, about ten minutes this Hitachi appeared from the city end, terminated in the Mooroolbark platform, with the second
carriage lit up rather than the first (didn't even know that was possible, unless my memory was playing tricks and it was the third car instead, but the communication door between carriages was at the Flinders Street end of the car, and it wasn't a D type car or the back three cars) and the driver absolutely floored it with an express run to Box Hill (this may or may not have supposed to be an empty cars run, but he let everyone on anyway, but we all had to get off at Box Hill), you could feel the whole carriage go down on one side and then the other when we raced through the old 60 km/h S curves at Laburnum (which have since been relaid with concrete sleepers, canted, re-rated to 70, and dropped under Middleborough Rd). To date this has been the fastest run I've ever been on when it comes to the Lilydale line; even the 2034 up express from Ringwood feels like a tram ride compared to this.
Slightly off-topic, but a lot of services beyond the wires run as 3 car Vlocity sets, do they count?