A myth is an attempt to explain mysteries, supernatural events, and cultural traditions. Sometimes sacred in nature, a myth can involve gods or other supernatural creatures.
The fact that the same sources that assert the existence of figures such as Abraham and Ishmael also state that an angel talked to Ishmael's pregnant mother and that the Sakina (a spirit sent by God) or Gabriel guided father and son to the location of the Kaaba, etc. make this story mythical.
Edit: I see your point, that mythology by definition implies the supernatural.
At the same time, we have events that had elements attributed to the supernatural, which did take place, and are historically documented. The two need not be mutually exclusive.
In any case, even the non-Muslim Arabs at the time also acknowledged this fact. As such, given that Prophet Muhammad, Peace be upon him, is a descendant of Abraham, Peace be upon him, and both are Muslims, it follows that they would have similar traditions, coming from the same source. Reclaiming the Ka'abah as a place of worship for Muslims is in accordance with this.