Incest in real life, is harmful for multiple reasons. There is genetic damage done to any children born of it. People have a natural aversion and disgust towards incest, for good reason. I suspect it is a form of inherited genetic memory. Our ancestors knew the dangers. Disgust can be a form of protection towards harmful behavior.
The second reason incest is harmful, is do to power dynamics. If one sibling is significantly older than the other, they could easily manipulate or pressure the younger one into unwanted sex. Plus, there is the societal and family shame.
In this work of fiction, we don't know if Kaede is able to produce semen to impregnate Chiaki. (She may not have testicles.) If she is capable of impregnating women, the author could solve the issue of genetic damage, by saying that Kaede growing a dick and Chiaki turning into a girl, radically altered both of their DNA. So much so, that there would be no risk of genetic damage to any kids they might have.
The second issue of power imbalance due to age difference, is non-existent. They are twins, and thus the same age. There is no age gap.
Societal and family shame are the only remaining issue. Incest is harmful to any children born of it. And society is right to discriminate against those who practice it. Incest is not something anyone is "born with." It's a choice. If Chiaki and Kaede go that route, they'll have to live with the fallout, or runaway somewhere, change their names, and pretend not to be siblings. The two of them trying to "change society's mind" about incest, would be abhorrent and harmful propaganda.
Incest can work in fiction, if it's not taken too seriously (the silly approach sometimes seen in hentai). Or, if it does go the serious route, then the characters need to suffer the consequences. I don't want to see any moralizing or lecturing from them towards characters that aren't accepting of incest.
The dangers of any work of fiction positively portraying incest, is that even if the author isn't trying to proselytize, their story can still have a subtle corrosive effect on people's attitudes. Fiction can portray events and people's behaviors in unnatural ways. Like they could magically have all the characters be totally cool with incest. It can be a form of escapist, wish fulfillment fantasy. Where the reader begins to think that people in real life should be just as accepting of incest as the fictional characters are.
Basically, authors can make attitudes, responses, and behaviors of people that would never, or rarely ever exist in real life, seem natural and the only morally upright options. They can even do so in a way that fits the story and characters. Most people in real life, have no idea how strongly we are effected by fiction. How many times have people used an instance of something that happened in fiction, to illustrate a point? Fiction shapes attitudes and behaviors.
It's only a mater of time before we start hearing the phrase "incest-phobe." Any argument can be won, by attaching the word "phobe" to the end of it. Perceived victimhood is a powerful currency. It can be used to immediately end debates (as soon as they begin), and silence opposing viewpoints. Why listen to what someone else has to say, that you disagree with, when you can just call them a "phobe"? And you can often use the platform you are conversing on, to get them banned for wrongthink against the terms of service, with the nebulous, vaguely defined, and ever expanding "hate speech". It's the perfect way to make ideas you don't want to think about, stay far away from you. A closed off bubble, where only ideas that support and agree with your worldview, are allowed to exist.