I will admit the strong likelihood that a Clintonista appointee in the D.C. District Court would use the reasoning you suggest to come out on Berry's side. But I would be willing to bet that the D.C. Circuit would reverse.
How does this lead to absurd results ?
The court would weigh all the evidence to try and see what the intent of congress was. I have no idea what the arguments were at the time of drafting this law but I bet someone is researching it.
To her credit she has the fact that when congress intended to limit appointments during vacancies in other situations they do it explicity. She also has the fact that the prior law had explicit limitations on vacancy appointments and that these did not survive the redrafting of the law. It would make it even more difficult to argue it was on oversight on congressional intent.