I don't think they're talking about intruders, but the person who lives in the same house with a gunowner, ie, victim is wife, children, partner, roommate, mother-in-law.
That is the inference of the article and apparently the researcher but apparently their data does not support that inference. This from the article in typical AP fashion is nearly in comprehensible. The study has several shortcomings. For example, the researchers said they could not determine which victims were killed by the handgun owners or with the in-home weapons. They couldn’t account for illegal guns and looked only at handguns, not rifles or other firearms.
My reading of it is that they don’t know who killed who or with what weapons. Only that someone in a home where someone owned a handgun got killed with a gun.