That said, if the defense can point out alternative scenarios, they only increase the doubt and thus chance for acquital.
The defense has done this. But the prosecution has never woven the evidence into a narrative that makes the least bit of sense.
For example, the prosecution says Amanda's DNA mixed with Meredith's blood is significant. But they don't explain why all of these samples were found in places where Amanda's DNA might naturally be present, while none were found in the room where Meredith was killed.
They say the luminol footprints were made by Amanda and Raffaele tracking Meredith's blood into the corridor. But they don't explain why there are only three of these footprints, why they form no trail or pattern, and why DNA tests came up negative on all of them.
They say the footprint on the bathmat was made by Sollecito, but they don't explain how he made it, or why he left it there for the police to find and examine. Nor do they explain why the big toe of this footprint looks nothing like the big toe of Sollecito's reference footprint but looks very much like the big toe of Guede's reference footprint.
They say Raffaele's DNA on the bra fastener proves he staged the crime to look like a sexual assault, but they don't explain why Guede's DNA was found inside Meredith's body if the sexual assault was staged by Amanda and Raffaele. Nor do they explain why this single DNA trace is the only physical evidence from the murder room that can be linked to Amanda or Raffaele.
They say the knife from Raffaele's kitchen is the murder weapon, but they are forced to add a second murder weapon to explain some of the wounds, and they can't come up with any plausible reason why Amanda or Raffaele would convey this knife to a place that was already equipped with similar utensils.
The defense can address all of this: The bra fastener is a fluke that happened because of poor handling of evidence, which real-world criminal investigators know is possible. The mixed DNA only proves that Amanda lived there. The luminol footprints are unrelated to the crime. The print on the mat was made by Guede when he cleaned up. The knife was never removed from Raffaele's apartment, and the putative match on the blade was an artifact caused by trace contamination in the lab, which again is a well-documented fact of criminal investigations.
Moreover, the defense can present a plausible scenario that explains all of the evidence. Guede broke in through Filomena's window. He was on the toilet when Meredith arrived home, which is why he didn't flush. He blitzed her and killed her with a small knife in the corner of her room, moved her body, removed most of her clothing, and sexually assaulted her. He cleaned up in the bathroom, and while doing so he removed his right shoe to rinse it off under the bidet, leaving a ring of blood around the drain of the bidet and drops of diluted blood in the basin. While his shoe was off, he put his foot down on the mat and left the print. He put his show on, went back into Meredith's room, spread the quilt over her body, and sat on the edge of the bed with the bloody knife at his side while he went through her purse. He took her money and cell phones, and he exited the room, locking the door behind him and leaving a trail of bloody shoe prints running down the corridor.