Mike1711 has clarified that rather than upholding them, the Marasca court was bound by them. That's a differing kettle of fish. To unbind those judicial truths required a more involved process, probably requiring the Unified Section of the ISC. As Luca Cheli observed, the Marasca panel was exonerating the pair anyway, so why make life more difficult for the courts?
Exactly. The Marasca panel
could have issued contradictory findings in its verdict, but that would almost certainly have triggered all sorts of complex judicial processes, including the very strong likelihood of the need to re-open Guede's case and Knox's case for criminal slander. Thus, IMO, the Marasca panel chose the "easy" route - while ensuring that its overriding job, the annulment of the murder-related convictions for Knox and Sollecito, was properly accomplished.
This also probably explains the sections of the Marasca motivations report which dives into hypothetical ("even if it was proven that more than one person committed the murder...." etc), which read like a conscious decision to sidestep the need to contradict previous SC findings. The bulk of the Marasca report makes it really very clear that not only does the Marasca panel deem that there's no evidence against Knox/Sollecito, it also believes that neither Knox nor Sollecito participated in any way (as evidenced, for example, by its derisory discussions of the practical impossibility of Knox/Sollecito either failing to leave any forensic trace of themselves at the murder scene or (more risibly still) being able to selectively clean away their own forensic traces while leaving those of Guede and Kercher).
I suspect that the judges on the Marasca SC panel, if asked what they believe factually happened, would say that the evidence - and lack of evidence - supports (and is entirely consistent with) Guede breaking in through Romanelli's window, entering a confrontation with Kercher inside the cottage, and assaulting/murdering her on his own before conducting a limited clean-up of himself and the scene and departing the cottage via the front door. But again, it needs to be pointed out that the SOLE remit of the Marasca SC panel was to assess the case (or lack of a case) against Knox and Sollecito. In that context, once it deemed - correctly - that there was zero credible, reliable evidence of Knox's/Sollecito's participation in the murder (and that the Massei/Nencini courts were unlawfully wrong to convict on the basis of fundamentally flawed and non-probative evidence/testimony), its job was done. It categorically was not the Marasca panel's job to give any sort of ruling on what factually might have happened, beyond ruling that Knox and Sollecito were not, in its judgement, involved.