I've got a suggestion for why Rudi was moved, but I'll start with my theory for why Marli's blood was not on the axe.
I believe he had an original plan that changed several times because he panicked.
His original plan was that he would be in the loo totally oblivious to the attack, in there for a long time playing a loud fighting game or music on his phone with his earphones in, the intruder also oblivious to him, as he had the door shut. He would have the probability of Rudi shouting and bringing the parents out of their bedroom. He would discover the scene. He would have the intruder bringing his own axe and leaving with it, because it was an intentional family murder, not a robbery, which means Henri would have to thoroughly clean the axe and put it back in the pantry.
I think what then happened was that after the attacks he cleaned the axe head, probably in the kitchen, but then a few problems occurred to him - what if he had left behind minute invisible traces in the crevices or in the wood handle - an intruder would not clean the axe and put it back in the pantry before leaving - perhaps more importantly - how could he remove the blood on his shorts and socks?- he wouldn't leave the estate to dispose of them in case he was seen, and a washed and bleached pair of shorts and socks would also be a give away.
So he devised a new plan, which would mean loading up the axe with blood again, and having the intruder leave the axe behind. Now he has to create a robbery scene too because the intruder didn't bring his own weapon, so it was an ad hoc attack on everyone who got in the intruder's way. He put the study light on and left a few drawers opened.
The blood on his clothing also created a few changes of plan. He would now have the bathroom door slightly open and Rudi being struck in bed but putting up a fight and struggling with the intruder in the bedroom closer to the bathroom, getting spatter on Henri.
The intruder would now see Henri with the open door and Henri would also now be attacked, but not with the axe (he couldn't face axing himself) so he took a kitchen knife back upstairs with him to cut himself in the bedroom.
Back upstairs he didn't want to disturb the blood scene on the wood floor where Teresa and Marli were lying because that would leave obvious patterns, and it would be easier to smear Rudi's blood on the axe from the bed and carpet, since he was moving Rudi anyway. He had clean hands from washing the axe and he dragged (dead) Rudi to the floor by his feet or lower legs, gravity causing the blood to pool on the floor in the same way that Teresa's blood flowed down the stairs when the EMS personnel moved her, he cut himself then went to stage the axe on the stairs, Rudi's blood got on the knife during this and left a smear print on the bottom corner of Henri's bed duvet so he pulled off the duvet to put it in more blood on the floor and try to confuse the scene.
I would say Henri backed out of telling this new version at the last minute, after moving Rudi. He would have to explain how he fought with the attacker without falling over Rudi who was already on the floor in that part of the room. At the last minute he decided to go with Rudi inexplicably moved there on his own after Henri left the room.
What Joubert hasn't picked up on (when he talks about staging) is that very little of Rudi's blood would have been left on the axe after it was swung around so much during the attacks on Martin, Teresa and Marli, and yet only Rudi's blood is on the hole in the stair wall.
I think Rudi's blood on the knife, which transferred to Henri's duvet while it was still on the bed, is a huge problem for the defence. On his version, Henri could have dropped the knife on the floor (after he pulled it out of his side) and Rudi (according to the defence still being alive) could have moved across the floor and bled onto the knife, but for a smear pattern to be created on the duvet on Henri's bed would mean having Rudi lift the knife off the floor and smearing it there, (leaving a blood-stained hand grip on the knife handle which was not there) or pulling the duvet down on top of the bloody knife, but then the knife would have been under the duvet on the floor and not moved to be under Rudi's bed. We see now why the defence has been trying to pin the movement of the knife on the police, unsuccessfully, and why the defence had their blood spatter expert Steyl conduct experiments for the smear pattern on the duvet - not being made by the blade of the knife but by Rudi's blood stained arm being pressed against a fold in the fabric, in the exact shape and size of the knife blade. Desperate times calls for desperate measures, obviously!
I'm really pleased that Joubert stuck with his firmly held opinion that Rudi was not alive and was dragged across the floor.