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"Kunigei" is a play on words. Although it's written in katakana (クニゲイ), the kanji for "Kunigei" should be "國藝" which is really just the shortened version of the manga's title "大國大学藝術学部映画学科" (Okuni Daigaku Geijutsu Gakubu Eiga Gakka). And it can also he interpreted as "Kunigei" as in "the Gay of Okuni University.
Why am I telling you this? Well, as far as the pun is concerned, the BL undertones in this manga might as well be intentional LOL.
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HE IS STILL HYPNOTIZED!!! IS IT REALLY NOT OBVIOUS?!
Being under hypnotism doesn't necessarily mean doing whatever the hypnotist wants. It can be as simple as "From now on, shitting under the shower is normal for you" and that's still hypnotism, even if the recipient is otherwise normal and functional.
In this case, he is still hypnotized into subconsciously thinking sex between brothers are normal. I mean, come on, it's pretty damn obvious. He may not be under heavy hypnotism like in the 1st season, but he. Is. Still. Under. Hypnotism.
ML hadn't confess, or maybe even realize, that he likes MC yet. Hopefully there'd be side stories exploring this.