Indeed, and despite his attempts at achieving otherwise, Gendo is not omniescent.
And by the virtue if introducing characters from other universes, you are forced to introduce the universe's 'ruleset', so to speak. IE. if you introduce a mage of some sort, you introduce magic as well. If you bring in Discworld's Death, you also bring in parts of its crazy logic, not to mention other forms of insanity(creeps from the Dungeon Dimensions?)
In short, strangely enough, it
could work, if done well enough. Considering that this is most likely a crack fic either way, some things can be handwaved, you know