it seems like people throws around the word rape so often they don't even know what it is...

this is a sadist to masochist moment. Basically the person will inflict "pain" but mostly just punish him by making him feel pleasured. So when the the seme said from the previous last chapters that he will punish the uke if he gets another injury. The uke had an injury was so confused and mind you not scared. He even said "yeah" and "can you really tell what i'm thinking". Then seme "punished" him and all he felt was pleasure but still confused because his past relationship was abusive. That's why he said "what will happen to me? will he punish me? ARE THESE THOUGHTS RUNNING THROUGH MY MIND," so the uke wanted the punishment but was just so confused because in his past relationship he was so scared of it but now he basically wants/not scared of it.