And yet you appear to be arguing that her conviction is perfectly sound.
And citing the fact that she and her brother both confessed in similar fact.
The very fact that torture was proven in court (even in the actual perpetrators could not be identified) would make me very cautious of being too certain of anything relating to this case.
My late aunt had a wonderful phrase which encapsulates the involvement of Leonor in her daughters disappearance, "flying with the craws". For non Scots this is the equivalent of joint enterprise.
My own personal opinion is that Leonor did not kill Joana but covered for her brother, indeed, in her last written statement she claimed to at last speak the truth and blamed him. It could be that they knew perfectly well that if João went down for another serious crime that he would go to jail for a very long time. I believe they concocted a first story that she had been abducted and then when that failed they concocted another story claiming Leonor had accidentally killed the girl. I think the truth is in there somewhere and that both of them are guilty. Only they know what happened.