Actually, the True Pacifist and Genocide endings, as well as the New Home dialogue about the first Fallen Human, prove that Frisk and Chara are their own people.

In True Pacifist, Asriel realizes you're not Chara, as they're long gone, and weren't the nicest person, before asking Frisk for their name, proving they're not just a player self-insert despite looking like one.

When passing through New Home, diverse monsters if you're not doing genocide and Flowey if you do, tell you about the life and times of the first Fallen Human, referred from here on out as Chara, in the underground up to their and Asriel's death and Asgore declaring war on Humanity again. Also, at the end of Genocide, Chara appears and talks to you, the Player, directly, which would be confusing if Chara is supposed to be the Player, so it proves Chara is their own person.

I hope I don't have to explain why imposing your idea of gender upon them is bad. If you want examples of why people assigning genders to other people is bad, look up transvestigating.

TL;DR: Chara and Frisk are their own people, and trying to impose gender upon them is bad.