Yes, a good point, it does. Breyer's opinion does say the court is arguing that the API is copy-righted, but used under fair use (as opposed to not copy-righted, in which case fair use doesn't make sense). But my point about what seems to be the main distinction making it copy-right-but-fair-use is the declaration vs. implementation concern, a distinction that logically exists (so I think the outcome is correct!), but does not seem to legally exist.
"We shall assume, but purely for argument’s sake, that the entire Sun Java API falls within the definition of that which can be copy-righted. "