Article 2 does not apply to Iraq or Afghanistan any longer as there is an internationally recognised government in both, so only Article 3 applies now.
The highlighted bits you pasted for Article 3 only apply to live persons afaik and not dead ones.
Equally enemy Taliban do not fall under any of those definitions, they are not civilians, and they are also not members of armed forces due to lack of uniform
As it is an internal conflict that isn't the case and only very limited parts of the Geneva conventions apply and only then to Afghan forces.
It applies because afghanistan is not an international conflict, it is an internal one fought with the arrangement of the lawful Afghani Government and as such Article 2 applies.
The Taliban do indeed fall under the auspices of the GC because the Allied countries decided that the, and I quote "Geneva Conventions and the additional protocols related to POW are refelective of customary international law, and will apply to the conflict with Al Qaeda and the Taliban, even if they do not apply as a matter of treaty law."
Excerpt from the Canadian Department of National Defence military Board inquiry into In-theatre Handling of Detainees:
“Common Article 3, so called because it appears in Geneva Conventions I – IV, provides the minimum standard of care, stating: In the case of an armed conflict not of an international character occurring in the territory of one of the High Contracting Parties, each Party to the conflict shall be bound to apply, as a minimum, the following provisions…(1) Persons taking no active part in the hostilities, including members of armed forces who have laid down their arms and those placed hors de combat by sickness, wounds, detention…shall in all circumstances be treated humanely… The Parties to the conflict should further endeavour to bring into force, by means of special agreements, all or part of the provisions of the present Convention. [131]
In support of this position, the CDS on behalf of the Government of Canada, entered into an arrangement with the Government of Afghanistan for the transfer of detainees. [132] This arrangement provides that the participants will treat detainees in accordance with the standards established in the Third Geneva Convention, designed to protect Prisoners of War.”
This was directly related to the handing over of detainees to the Afghan Government.
Article 2 has become relevent since the Afghan Government became a signitory of the GC and as such has become the High Contracting Party and the NATO/ISAF forces are Invited State Forces which makes the Afghan war a non-international conflict between it's Armed Forces supported by the invited forces against dissident armed forces or other recognised armed groups within it's own territory. The problem arises because the Afghani Forces are not doing most of the fighting and thus negates parts of AP2, thus the emphasis now on including Afghan Forces in all major operations to bypass this.
I will agree that there seems to be quite some legal rigmarole going on here to make this stick, but as with most things, if the strongest parties agree then it is ratified and legal.
As for the AP3 only applying to living persons, it does not, because of the first provision:
"Persons taking no active part in the hostilities, including members of armed forces who have laid down their arms and those placed hors de combat by sickness, wounds, detention, or any other cause, shall in all circumstances be treated humanely, without any adverse distinction founded on race, colour, religion or faith, sex, birth or wealth, or any other similar criteria."
This was applied to the inhumane mutilation of corpses in conflicts in Bosnia and Africa because of the
"any other cause" criteria. So can be applied here.