Troy Baker is not Word of God. He's said he voiced Kanji from the mindset that he's gay/bi, but that's just how he got into character. Kanji is a complicated character just like Naoto, and just like Naoto, people misconstrue the meaning behind his characterization. Naoto is upset over not being a man, feeling that's holding her back, but through the game and her social link, she learns that it's not her gender that matters, it's that she's happy being the best person she can be, regardless of gender. It basically is a middle finger to transgenderism by saying that your gender means jack-squat. It's who you are as a person that makes you. If you're a sucky man, you're gonna be a sucky woman, and vice-versa.

For Kanji, it's very similar. It's not his orientation that defines him, or his hobbies, it's how he treats others and the person he is. He's confused when starting to interact with Naoto, which some people would like to chalk up to him liking a "guy", but let's remember science... Teenage girls, regardless of what type of clothes they wear, will exude female pheromones. Which attract guys. Kanji could easily liked a male Naoto as a friend, but those pheromones were telling him some other things and saying "You like this person", which confused this straight guy as he wouldn't like a guy normally. Which we find out, he never liked a guy there. He liked a girl.

If anything, the whole "Kanji is gay" argument is insulting to both tomboys and girls who wear their hair short and wear more unisex clothing. It's basically saying that you aren't a girl or that only bi/gay men will like you because you look like a guy. From everything we can tell from our available material, and with no Word of God to say otherwise, Kanji is straight. His sole love interest is a girl. He may be a softer guy under his hard exterior, but that doesn't make him gay either, just a sensitive straight guy. And there's plenty of them out there. Many just still hide it similar to Kanji because otherwise they'd be labeled things like feminine or gay, just like what incessant fanboys/girls insist on doing with Kanji.