I disagree. However, I am not aware of any caselaw on this point. It is an interesting logical twist you have added, but I fail to see how it must be that way in view of the fact that copyright explicitly allows clean-room type reverse engineering.

The legal status of reverse engineering is not at all clear-cut. There are many nuances depending on the circumstances, and much of it is determined by case law rather than statute. There's no clear basis for you to make claims about how this new class of copyright (on APIs) will interact with reverse engineering. However, it is much simpler to state that if APIs are a work subject to copyright, then it must be possible to make derivative works of APIs that are also subject to copyright absent any explicit exception or fair use right.

You have not at all established this point. What makes you think that the API of a reverse engineered implementation is not tainted by the copyright of the original API? It's clear that clean room reverse engineering produces an independent implementation, but it also seems clear that such a technique does not prevent the structure, sequence and organization of the original API from strongly influencing the structure, sequence and organization of the reimplementation's API.