To the extent that it's relevant here, that appears to be untrue. This hinges on the fact that with an API, you have to match it exactly, and there's no reasonable way to argue that someone could sit down and do a clean room implementation of the Java APIs that perfectly matched all 3000 classes and all the public interfaces of all those classes.
You can do a clean room implementation of the Java Platform, but you can't do a clean room design of the Java APIs. The whole point you're trying to solve is to make something that's compatible with Java, and that requires knowing the Java APIs, i.e., it's not a clean room. If we extrapolate that back to IBM and clones, as long as the clone makers must come up with the same external API as the IBM BIOS, then this court would say that IBM absolutely could use copyright law to prohibit clones, because the clones would have to have copied the APIs -- not the code, but the names and types used in the APIs themselves, and IBM holds copyright to those names.
Coypright covers derivative works of copyright-protected works, as well as literal copies. If APIs are copyrightable, there is a very good case to be made that a reimplementation of an API implementation (not an API that serves a similar function, but an actual reimplementation) is a derivative work of the API itself.
The Copyright Act, however, is; if APIs are protected by copyright, than making a derivative work of an API is an exclusive right of the copyright owner.
Which is a key reason why there is widespread concern about the CAFCs ruling on API copyright. (OTOH, Google losing on fair use at the CAFC makes it more likely that the API copyright issue gets to the Supreme Court in this case rather than a later one, so it might be a good thing for resolving that concern.)
No literal copying of text is required for something to be a derivative work. Transforming a work implementing an API into documentation describing the API would produce a derivative work of that API, if the API is protected by copyright. Transforming that documentation of the API into another implementation of that API would also produce another derived work of the API.
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.