When people say this series feels "rapey" they don't mean rape is actually occurring they're more talking about Hishikawa's relentless propositioning of Komaki despite being rejected pretty unequivocally which IRL is literally just sexual harassment and shows a complete lack of respect for her boundaries. Like in the real world her behaviour would be wildly inappropriate and some readers can't suspend their disbelief enough for it to work as comedy as it's intended to here. Also, ew don't be gross respecting someone's blatant refusal of your advances is not some ridiculous draconian standard of conduct it's basic respect.
Quick question. What boundaries is Hishikawa crossing? Komaki seems pretty chill about this whole situation. Its not even presented that it is Hishikawas interest that she is rejecting, only her methods.
Readers are having a far more exaggerated reaction to a fucking joke than the target character, so much so that they are already calling rape when absolutely nothing close to it has happened.
Of course Komaki is chill she's the archetypal straight woman designed to act as a foil to Hishikawa's absurd shenanigans. That's literally her narrative purpose. Most of the people taking issue aren't put off because of how this affects Komaki (because she doesn't exist) put rather because they are responding to Hishikawa's actions with the same reaction they'd have to them in reality: disgust. The fact that a fictional character designed to not take offense to an action does what they were literally written to do doesn't make that action inoffensive. For example, Bella in Twilight being a-okay with Edward breaking into her room in the night without her knowledge to watch her sleep didn't suddenly make that not an insanely creepy thing to do.
People are allowed to express distaste for a joke they think is unfunny and inappropriate. Something being intended as a joke doesn't exempt it from being subjected to critical thought.