That is a circle that takes some squaring, but I am not that surprised the PL ended their investigation with a list of unanswered allegations (I have done that myself many times: this is as far as we can go, this is the list of unanswered issues and possible breaches, do we proceed?). What surprises me more is that they went to the disciplinary process with all the allegations.
Let me explain.
Their investigation reached the point where they had gone as far as they could with the accounting records and supporting documentation available at the club. They needed external information to conclude on each of the matters but the club refused access, or claimed that the third parties refused access. I have previously given my thoughts on why the club would take that approach.
So the PL had to either drop the case for a lack of evidence or proceed with the allegations in the disciplinary process. This would be a wholly unsatisfactory position for the PL because they knew evidence was provided to CAS that they didn't have access to. Evidence that would have clarified some of the issues. So what could they do? Dropping the case would set a terrible precedent on cooperation. Continuing the case would likely lead to defeat when the counter-evidence was presented. In the end, though, I am not surprised they decided to refer the club to the disciplinary process.
But the question of what gets referred is where pressure from the cartel comes in. The investigation may have had 115 unanswered issues but, basically, there is one, single issue that could have been referred, two including non-cooperation. There was no need to refer to all 115 as separate allegations because almost all are either immaterial or consequential to the main allegation. In whose interest is it to have as much coverage given to all the allegations? And who is too weak to stand up against it?
Anyway, just my thoughts :)