Your forgetting that he fought against a member of The Organization (Xemnas) in Hallow Bastion previous to his travels in Castle Oblivion and then he seen Marluxia on the grass path. And now he sees him again.
To Sora there all the same person since he was clocked. So Sora saying "thats it" kinda makes sense.
Hes getting tired of getting dicked arround by this clocked figure and there riddles.
You actually make some sense.