I don’t think there is any ambiguity. 5 USC § 3345 defines three classes of government employees eligible to temporarily perform the functions and duties of a vacant “advice and consent,” office. The first two are iffy, perhaps, but Whitaker clearly qualifies under the third.
Whitaker served as Chief of Staff to AG Sessions immediately prior to Sessions’ resignation, and the default and automatic first rule is that when an “advice and consent,” office becomes vacant, “the first assistant to the office,” becomes the acting officer. See §3345(a)(1).
The term “first assistant to the office,” is not defined in §3345, and perhaps the administration might argue that the Chief of Staff is the “first assistant.” But this would seem to be scuttled by 28 USC § 508, which provides specifically that for the Department of Justice, “…[F]or the purpose of section 3345 of title 5 the Deputy Attorney General is the first assistant to the Attorney General.”
The second possibility is that the President may ask any other “advice and consent,” officer to serve. The Senate approved Whitaker as a US Attorney, but I agree there’s a time and function argument to be made there. Fortunately for Whitaker, if not for the rest of us, the third category is one under which he clearly qualifies.
The third rule: the President can select a senior “officer or employee,” of the same executive agency, if that employee served in that agency for at least 90 days during the year preceding the vacancy and is paid at a rate equivalent to at least a GS-15 on the federal pay scale. §3345(a)(3).
That manifestly covers Whitaker, who has served as Chief of Staff since September 22, 2017, a position that’s on the ES scale, and thus above a GS-15.