Okay the MC is definitely the ones who did the misunderstanding...
I am just going to say this: creative people are very proud of their creations, they don't usually take advice from people they don't respect.
So the fact that the MC takes that criticism from the assisstant on the first day of work is the most unrealistic thing.
Here is how a normal person should have handled it: "okay, thank you for the feedback. I will take it into account for reference later. But right now we have a deadline and we need finish this and not get hung up on the small details."
If she is very arrogant and even more insistent I would try to say: "Look, I appreciate your passion for the Manga, but let's be realistic here, the manga is not real life. No one looks like this. Very few act like this. We are just using the manga as a medium to tell a story and sometimes we need to insert these tropes in the manga to keep people entertained."
If she is even more arrogant to the point of stubbornness, then I would have to go boss mode. "Look, you were hired as the assisstant of the artist/author. I am hired as the artist/author. Whether what I do is realistic or not, it brings people joy and the company sales. If you think that you can do better then try striking out on your own. But right now, either help me finish this as was intended or stop getting in the way and go home."