Basic context: speaker 1 is asking about speaker 2’s gender. Speaker 2 is some kind of a creature that has no gender but can mimic other living things, and in this case it’s a human. 「今更だけど、お前は男だったんだな」 「おとこってなあに?」 「それがついてるやつのこと」 「んんー、よくわかんない。ご主人さまのマネしただけ」 「待て、俺のはそんなに小さくない」 I don’t understand the line in bold. My guess for it is “It might be late to ask, but you’re a male, right?” “What’s Male?” “I’m asking about what’s there.” “Hmm, I don’t quite get it. I simply mimicked Master.” “Wait, I’m not that small!”
I think I think your translation the closest , he's basically saying the stuff down there that a guy is suppose to have. So edit your sentence. "I'm asking about the "thing" thats down there" something along that line.
You've got the right idea, just needs some tweaking to make the conversation easier to understand: "Kinda late in asking, but you are male, right?" "What's "male"? "Someone with that thing down there." "I dunno what that is; I was just mimicking what master had." "Hold up, I'm not that small!"
But how do you know it’s a novel I’m currently reading? There’s so many BL, I don’t have time to read them all, and many go under my radar. Unless you’ve seen me comment on your translation?