I went through the document I tried to look at which articles are actually respecting the Geneva Convention and which are not.

Be careful, some articles are mix: as S2 Art9

In accordance with Geneva Convention
S1 art 2, 4,.
S2, art 8, 9, 11
S3 art 14, 15, 17, 18, 19, 20*
S7 art 36, 41
S11 art 50, 51,
S13 art 64

Not in accordance with Geneva Convention
S2, art 9,10,
S3 art 13, 19, 20*
S 7 art 36, 41

*I suspect traduction error or imprecision.

What I think is interesting is the negative approach of Law and Right in that document. Where a western document will say that authority has competencies to judge such issues, they go by that issue cannot be judge by any other authority. (see S9 art 43 as example).

Mike, we can argue long time and you know that. There is whole bunch of layers working on that at ICRC.
Unfortunately, I am not in position (I do not have access to all my material) to come with illustrated argument. But the detention of terrorist without status, either or comon right or prisoner of war is a denial of the Geneva Convention.
Also, the absence of compensation for the individuals that were not recognised guilty of any crimes. This is in opposition with Geneva Convention. I would say Geneva Convention it self (1949) and the 4th protocol on civilian populations.

My point is that if you want to take for strategic base of you legitimacy the rule of law then you have to apply rule of law. If you declare that Rule of Law is what you promote, then you have to apply it also.
If you start, even one time to argue that you will not apply the Geneva Convention to one category of population and purposely do it without legal frame work then you create a precedent. In Anglo Saxon law, if I do not mistake, the custom prime on the law. So if you introduce a new custom then you create a new legacy. That you may or may not formalise by a normative act as a law. But still you do introduce a legal practice and then endorse it.