Kaz inquires, asking "What about him?", referring to the medic, so it's of some concern to Kaz, and he is told about the shrapnel in the medic's head, so it isn't a case of not noticing. He's loyal to his men, the MSF survivors in particular, so I don't imagine him deciding "Hey, well fuck shrapnel head".
It's explainable, but it should have been addressed or avoided. Yeah, Kaz could have forgotten that it was actually the medic who had shrapnel lodged in his skull. Perhaps he was told that the medic was dead, so he never put two-and-two together. But it's just another element that highlights how badly executed the twist was. If you want to pull something like that off you need to do it well; having to pick and choose which parts support the twist and which don't weakens it as a whole.
No, I don't think that's the case. Kaz never suggests "you aren't the Big Boss I remember", which would have been a good way to introduce the possibility of the twist. It's clear he wholly accepts the medic as Big Boss, even accepting his authority, and is only made aware of the real Big Boss having abandoned him in the post-credits sequence.