There is no reason that DOJ rules of succession would take precedence over Congressional legislation creating actual, legislated, rules of succession.
That's a valid point, and I've said many times that the DOJ rules of succession are arbitrary in nature and subject to change at the discretion of the President anyway (he's done it twice since he was inaugurated in January 2017). But there are no "rules of succession" created by Congress in this case. The Federal Vacancies act outlines temporary appointments the President MAY make -- which clearly indicates that he is also free to leave offices vacant if he wishes.
Also -- Keep in mind that the conflict between the Federal Vacancies Act and the U.S. Constitution only exists for "principal officers" under the Appointments Clause. If Whitaker had been appointed to a post like acting Deputy Secretary of the Treasury, this wouldn't even be an issue.