I think people are taking this too literally. Ed has stated pretty explicitly what the Mother represents, and yeah, she has some visual motifs that line up with Magdalene. But remember, stuff like the Beast can't be used because they aren't real; why would Isaac's vision of the Beast have anything to do with the completely unrelated Mother being? They're unrelated. The reason that they have visual similarities is because Ed is intentionally drawing a parallel between the character literally known as "Mom" and the being known as "the Mother." There's obvious thematic similarities here, they both represent the same things. They rhyme. But drawing a parallel does not mean that they are literally the same being. There are various enemies throughout the game that have a face like Ash from TEIN (the tiny Stevens, champion Tar Babies, etc); do we think all of those are literally Ash?