Just because the person asking the question isn’t aware of they’re implicitly making that assumption, doesn’t change the fact that a logical assumption has been made. It just makes the questioner ignorant of the assumptions they’re making.
Personally don’t totally understand the argument being made in the paper. But I can understand the idea that I can ask a question, without properly understanding the assumptions I’m making when asking the questions. Indeed I can also understand that I might not even notice the assumptions I’ve made with my question, and why that would make my entire exploration and conclusion invalid, _after_ doing the investigation. Logical fallacies can be really difficult to spot and understand.