[The writers of any legislation riddled with the phrase "... the Secretary may..." because the democrats who wrote it, passed it, and put it into force should have considered the possibility that the next Secretary might not be a democrat.]
Perhaps that is part of if not exactly why they wrote it.  Politics and legislation is rife with unintended consequences as part of good intentions.  There are also considerations of workload offsetting while retaining oversight. 
Also, it is important to note that the policy making process of the ACA was over a month with dozens if not hundreds of amendments proposed by Republicans being incorporated in the ACA during the process.