There is a difference between שכב אותה and שכב עמה (lie with her): שכב עמה includes lying down even in an unnatural way, while שכב אותה indicates lying down precisely in the natural way. And any place where it speaks in a way of modesty, it will use the language שכב עמו.

And with respect to lying with a male, the language שכב את is not correct, and from this the sages of blessed memory conclude that when it is written את זכר לא תשכב (You shall not lie with mankind, as with womankind)⁷²⁶, it is a warning against lying down with another male in the passive way.

footnotes: ⁷²⁶ Leviticus 18:22.