The MC does say that it was still rape even though it was just the 2nd base (during his musings the day after in ch5), but excuses the ML because technically the ML is a "newborn".
Also, a lot of people irl (mostly men) does not consider it rape if there's no penetration going on and this is more prevalent in East Asian countries sadly. Heck, a lot of Japanese men (and women) does not even consider it cheating when the men bang a hooker despite them being in a relationship-- you can imagine what sort of shit is on the Japanese side of the internet that the ML "learned" from. The fact that he asked for consent before entering was a small mercy as it is.
Plot-wise, the somno thing became a factor why the MC's belief that the ML does not really knows what he wants solidified. I hope the author expanded on it more though but it was rushed at the end. Maybe if this had 2 volumes, the pace would have been nicer.
The sleeping assault was still assault