Apparently this line was actually about Komaeda's personal hygiene, not his general looks.
"Komaeda cares about hygiene" canon. I knew it.
Waves. I hope you don't mind my adding on to this.
In my opinion, the conversation goes like this:
Mikan: Um...besides that, I thought Komaeda-san looked too kempt...
Nagito: Ah! This is the first time I've been complimented for my appearance! Like, even my own mother never complimented me on it, you know?
But I can see where the confusion/differences arise. Breaking it down literally...
Mikan: Um...besides that (i.e. "besides the fact the murder weapon's diameter is off, absolving Komaeda"), I thought, "Wow, Komaeda-san looks clean/pretty".
Mikan specifically uses キレイ which means "clean" as in spotless, tidy, etc. but also means "pretty/beautiful". This makes Komaeda's follow up line make a lot more sense - he thought she was calling him pretty. (hence me changing the word to kempt to keep the ambiguity).
Nagito: Ah, this is the first time in my life I've been complimented on how I look. Like, even my own mother never gave me a compliment!
Firstly - just a fun thing to point out - Nagito uses すら here instead of さえ. Both mean "even" as in "not even [...]" but さえ is used more by people. Many people will say that they are interchangeable (with grammatical differences of course) and that the only real difference is that すら sounds more literary. But I'd argue (and a lot of other people) that すら sounds more powerful. It gives the added impression of "(not) even [...] (and that's crazy, right!?)"
Anyhow, Nagito specifies "outward appearance", which could refer to being called pretty or clean. The second line doesn't really clear that up. Japanese is very context based however, so when he says (lit) "(the implied action of speaking) a complimenting thing was nonexistent (even from my mom)" that "complimenting thing" - while very much can just be translated as "my mom never gave me a compliment" - I feel is pretty obviously supposed to be "my mom never complimented me on this subject". But it's ambiguous.
I feel it's the latter though not just because of Japanese being context-based, but because it's the whole point of the joke in the scene. Nagito thought Mikan was calling him pretty.
But, I do have some good news for you! Nagito being a clean freak IS canon, according to the art book.
There's a fun section where Monomi makes comments about everyone's rooms. This is what she has to say about Nagito's Bathroom:
His bathroom is super sparkling clean! After every time he uses it, he scrubs it down with cold water to prevent mold from growing!
Sounds excessive, Nagito...
This came up in a rare vanity google search and made me log in to tumblr for the first time in like 15 years, but I want to clarify some things. There's a joke in this exchange. The joke stems from the double meaning of kirei in Japanese, which does not exist in English. Mikan's line, besides setting up the joke, is also important to the mystery (that is, it's what should be *kept as literal as possible* because it's important to the story). That is to say, Mikan has to say Komaeda was clean. "Kempt" does not work. It's not a word people use. Mikan would not use it here, and you can't convince me otherwise. So the question is how we can save the joke. We *can't* be literal - it would destroy the joke, make the exchange make no sense, and end up being far more inaccurate than other choices. We can write a different joke so there's still humor in the exchange, but changing the basic idea completely is something I'm not a fan of. So we went with Komaeda thinking Mikan complimented him on his hygiene instead of on being pretty. This is still a different sense of "clean" than Mikan was using (granted, closer than the two senses of "kirei"), so I feel like the joke is basically (though not literally) the same. I honestly don't think we could've done any better. Translation is a war to be accurate when accuracy is impossible. It's an art of compromises. There will *always* be compromises.
