In "common parlance", "literally" means both "literally" and "not literally". "Common parlance" has become a joke of a language used by idiots who don't actually speak English. In English, a cat won't ever be a dog no matter how many confused people use the wrong word.
And no, "vagina" specifically refers to the flesh tunnel between vulva and cervix. A penis is not a scrotum, a vulva is not a vagina. Get some basic sex ed, for fuck's sake.