The telephone game of people with the weirdest subjective interpretations of the new update and people that have not played the update (or maybe even the game at all) going back and forth making up increasingly uninformed reasons to criticize the story is unsurprisingly producing some terrible takes.
Riko's concern with his masculinity doesn't come from a place of wanting to be all the things that make a stereotypically "manly" person, but from his lack of confidence in everything else about himself as a person. He feels incapable of defining and asserting himself as any kind of person because he feels that he is unremarkable or a failure at everything, so he attaches too much of his identity to the one thing he is biologically pre-assigned to be: a man.
Now the problem is, it is already plenty unhealthy to cling to your biological sex to be the entirety of your identity even if you are somewhat compatible with the social expectations tied to it (looking and acting "manly"), but in Riko's case he is just not, he has a very feminine body and a very bashful attitude. Even without any malice behind it, people will accidentally mistake him for a girl or struggle to see the fact he is a "man" as his most important trait and defining of how they should treat him. This leads to Riko feeling like he is failing to assert himself as the one thing that should be impossible for him to fail at, which further craters his self-esteem.
The advice he receives and the resolution he reaches in this last update is that he should develop his sense of self, he needs to figure out what are the things that he likes, have new experiences, and grow the parts of himself that make him happy and proud of who he is.
Riko needs to stop fixating so much on having other people see and treat him as a "man" first and foremost, and instead he needs to work towards having other people see and treat him as Riko, the whole package of a person. But to do that he first needs to figure out himself who "Riko" really is, what are his interests, his desires, his values. Once he knows and develops confidence on who he is, from that exuding confidence people will be able to see who he is and treat him accordingly, and that will gradually improve his interactions with other people and make them grow more pleasurable.
Lengthy character analysis done, I will once again state that this game doesn't have a single meaningful choice, it is a linear story where at most you can do some events in different order, but they play out the same. With that context I do not know how some people can say the game is "ignoring" or "betraying" the player's choices...what choices?
Also idk why some people are making such a big deal about Riko doing anal masturbation for the first time when it was already pretty established he is aroused by dicks and is surrounded by futanari girls that would put most pornstars to shame. Seems like a weird thing to be shocked or disappointed by, where else were some you people expecting the story to go?