What objective evidence put them there?
The repositioning of the body lends itself to the multiple assailant theory, which lends itself to the evidence surrounding the burglary - the rock easily could have been thrown from the outside by Amanda/Raf the morning after, there was no evidence that Guede actually climbed through the window, much less was ever in Filomena's room.
So we've determined that there necessarily was multiple people involved and the burglary was likely staged given the lack of garden dirt in Filomena's room.
Of everyone that has a key to the front door, only Amanda has no alibi. If she had a valid alibi, why has it not been presented? The one alibi she came out with, Raf called rubbish. So that's obviously not the truth. She's on trial for murder, nothing else she could have been doing illegally would bring the same sentence.
We also have Amanda's bloody footprint in Filomena's room - the one where the blood is Meredith's. If Meredith's room was locked by the assailant, how did Amanda get enough wet blood on her foot to leave a mark at the time she said she arrived home?
I would still argue that Raf's DNA on the bra clasp is relevant. His DNA was found nowhere else in the cottage (aside from the cigarette butt). Even if he didn't touch the clasp directly, how did his DNA get into the room but not on the door/door jamb/elsewhere that was swabbed?
The footprint in the bathroom that FoA attempted to attribute to Guede is actually a better match to Raf's footprint (as the powerpoint that was linked previously in this thread demonstrates).
That puts Amanda and Raf at the cottage at some point while Meredith's blood was wet. Even if they didn't kill Meredith themselves, they were certainly involved in the "cleanup" (i.e. mopping of the floor, repositioning of the body, etc) which makes them just as culpable.