Mordred is the son of Roland/Susannah and the Crimson King/Mia. If you hold with the Marvel comics additions, the Crimson King is the son of Arthur Eld, conceived through trickery (Maerlyn) with the Crimson Queen.

The Marvel Comics (with King's blessing) stated that Walter is the son of Maerlyn and Selene, Dark Goddess of the Moon - and that he was only given over to his human parents to learn the ways of men.

The comics do present some plot holes compared to the books though. Given the nature of the story, you can at least hand-wave these away by claiming that they happened on a different go around.

While Mordred was not my favourite character, it was absolutely plausible that a creature described as one of the last miracles spawned by the Dark Tower could undo Flagg.

Don't forget, Flagg was also wearing a "thinking cap" which by his own ission stymied his own powers - as a (useless, it transpired) protection against Mordred. I liked that part actually. Proof that the Prim would always hold more power than technology.

Flagg/Walter's preening arrogance and hubris (not characteristics invented on the spot - he had always been full of himself) did the rest.

Due to the nature of the Dark Tower (also what he says to Roland in DT1), it is entirely possible that he is still out there in the King-verse somewhere. Will he learn his lesson? Who knows. Maybe he and Roland are much more similar than they'd care to it in that regard.