I don't take LD seriously. It's meant to be a comedy and animation has a very hard time to cross over into live action.I get that it was probably the result of mashing together planned plotlines due to the impending cancellation but the "Section 31" multiverse rift mission in LD was a bizarred choice that seemed to have very little to do with S31 as an organization.
Unless Mike Mcmahan has said anything about his reason to put William in charge of the mission and make him S31, I assume it's just a concept that he thought was funny and he made it work.