Re: The lower courts backed Google; whoops!
The clean room implementation still has to be an implementation of the API and it's the copyrightability of the API that's the issue.
Why is it an issue? Well, look at a C program. At the top you'll see a lot of #include statements. They're copying various files into your program. What are those files? They're parts of the system's API. The same thing is apt to apply in other languages.
Any program being compiled incorporates at least parts of the API(s) it's written against. To raise any form of copyright issue against those is very worrying for the way in which the entire software industry works which is why pretty well the entire set of big players in the software industry apart from the principles have weighted in with amicus briefs. You should at least consider the possibility that they know what they're doing in spending money on lawyers to do that.