@zStella Oh, I feel you. I had similar issues when I used to translate for a mobile gaming company last year. The last big issue I had with things I couldn't translate well was the way the main character called her love interest. In Japanese, she called him Saku-san, but I was made to remove all suffixes from the translation, so she called him Saku in English. Problem is, by the very end of the script, on the best ending route, the guy asks her to drop the honorifics and call him just Saku. I thought about going back the 40 thousand lines and changing every instance of her calling him Saku to Mr. Saku, but then there was the foreigner guy that called him exactly that, and the way he called him was part of his character quirk. Not to mention I didn't have enough time to come up with something (two months was not a fair deadline for such a huge script), so I had him ask her to give him a pet name, "now that we're going out".
But if I were translating the manga, I would have done what you wanted to avoid doing and make use of translator notes. A fan translated manga is far different from a visual novel, you can take advantage of the media to add a glossary page at the end, or even short comments on the white parts outside the framing. My translation method is a mix of making the conversation sound natural in the target language and teaching the source language for those who want to learn (that's how I started learning Japanese back when I was 12, thanks fansubbers that left ohayou, itadakimasu and shikon no kakera as is, you gave me courage to start studying the language), so I see T/N as advantages instead.
But if I was going to adjust my translation to your ideal, I would have went with something like this:
-Are you... a natural (superhero)?
- (Geez, you're such a natural airhead...)
She still doesn't make her question clear and he still takes it the negative way, and the conversation sounds a bit more natural. Some alternatives would be "Were you born like that (a superhero)?"/"(Geez, you've been an airhead since you were born)" or "Have you always been like that (a superhero)?"/ "(Geez, you have always been an airhead)".
The problem with localization isn't translating, but rather making the meaning understood while making the script seem natural. It's not an exact science, even professionals who spent decades on the market still suffer with this. Keep it up, though, I'm enjoying this series, and you're doing a good job with the translation. Sometimes those hiccups are inevitable (but hey, at least you don't have to deal with a deadline).