Now, we finally get to your case. No, it does not afford protections to people who intentionally violate the convention who have not signed on. Read it again. They must make the fact that they are a soldier apparent to the best of their ability. Clearly, the terrorists do not do so, at least in every case which would then mean you will have to prove exact situations where the enemy combatant did in fact make their status as a soldier apparent to the best of their ability and you would need to prove that torture was used on that person. And, of course thats not even going in to debating what is and isn't torture.

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Qur'an:8:39 Fight them until all opposition ends and all submit to Allah.
Qur'an:8:67 It is not fitting for any prophet to have prisoners until he has made a great slaughter in the land.
Qur'an 8:12 I will terrorize the unbelievers...Strike off their heads and cut off each of their fingers and toes.
Qur'an 9:5 Fight and kill the disbelievers wherever you find them, take them captive, torture them, and lie in wait and ambush them using every stratagem of war.