Here's my theory on what happened.
Around 8:30pm Rudy arrives at the cottage (From CCTV footage), most likely to see the guys downstairs. He's broke and looking to score some pot for free from them (We know he was broke and that the guys downstairs were growing dope plants, used it, and that Rudy had been around before.) Finding no-one home he gets it into his head to break in, but with the windows all gilled he decides that the girl's place will have to do, after all he knows that they are close to the guys downstairs and so might have some dope and perhaps money that he can take.
Noting that the balcony is well lit by street lights and visible from the road (you can see this in the photos, video, and on Google Maps Street View), he climbs up and pulls open Filomena's shutters (as shown by the defence demonstration), pushing them fully open, then makes his way back up to the car park area, selecting a reasonable sized rock (which later will be found in Filomena's room) he lobs it through the window (this explains the final placement of the rock as it is already travelling angled towards the left looking in the window. It hits the inner shutters denting the wood and leaving glass in the dent, throwing the shutters open and scattering glass across the room. The shutter deflects the rock further to the left resulting in it falling beside the wall in the bag, which then tips over.) He then waits to see if anyone heard it knowing that he can head up the driveway if a light comes on. Seeing no-one, he climbs over to the top of the guy's window and started removing glass and putting it on the sill, then when he can reach through to get the latch he does, scratching his arm in the process leaving the blood and hair that were never tested. With the window open he is able to climb up and through. He steps on the TV cable pulling the TV on top of the wardrobe, then making it inside, he pulls shut the outer shutters and closes the window.
The time is now about 8:45pm. Rudy knocks over the laptop looking at that, but knowing the trouble he had fencing the Lawyer's one decides to leave it, and rummages through Filomena's bedside table instead, looking drugs or money (seems to have been disturbed in the photos). He then heads out of her room and into the lounge, stops at the fridge for a drink of orange juice, and moves onto Laura's room when he searches through her dresser drawer (which is open and looks disturbed in the crime scene photos.
It's now about 9.00pm. Rudy gets a call of nature and heads to the loo in the Italian girl's bathroom.
9:05pm Meredith returns home unaware of the intruder inside. She might find the lights on inside and think that Amanda left them on when she left for Raff's. She heads down to her room planning to get out the books she was going to study and re-ring her mother (which she did around this time each night and had just failed to be able to get through based on her phone's history.)
~9:06pm Rudy now knows that someone is home. He can't afford to disturb them and risk getting caught, so doesn't flush. He heads out into the lounge and to the front door, but finds it locked (The door had a habit of coming open if just latched so the girls had to keep it locked to prevent this. It is unlikely that Meredith would not lock the door because she was supposed to be going to bed as she was tired according to her friends.)
~9:07pm Rudy realises that the only ways out are either via Filomena's window, which he doesn't want to risk a fall from, or by confronting whoever is home. Getting out his knife, he opts for confrontation.
~9:08pm Rudy enters Meredith's room catching her by surprise. A fight ensues. Which Meredith is strong and puts up a good fight, Rudy has size and muscle on his side, and is able to overpower her grabbing her hair, slamming her head against the wall. The fight culminates with Rudy throwing his body weight onto her from behind and stabbing her in the neck to stop her screams. Meredith collapses beside the wardrobe, bleeding heavily, blood from the wound being aspirated over the wardrobe doors. (The state of the room, blood and wounds tell the story of the fight.)
~9:12pm Rudy collapses on the bed placing the knife down on the sheet leaving the bloody imprint. Realising what he has done he gets up and pulls Meredith's jacket off (DNA on clothing), then tries to push her t-shirt up to stop the bleeding. When this fails he goes and gets towels from the bathroom and used them. He grabs Meredith's Bra strap (DNA located on bra) and hauls her into the middle of the room, ripping the strap and clasp from the bra, exposing her breasts (this is shown by the blood drops aspirated onto her breasts after she is moved and the bra torn off.)
~9:18pm Perhaps turned on by the fight and seeing her naked breasts, Rudy decides to assault Meredith as she dies, pulling down her jeans and panties, putting the pillow under her hips and violating her (DNA found inside Meredith) before ejaculating onto the pillow (semen stain on the pillow)