Nothing in that case suggests that using an API is infringement. It's about re-implementing an API for a different purpose. So using Twitters API is fine, but copying Twitters API for use on a Twitter clone service, not fine.
I also don't think this case necessarily prevents re-using an API for interoperability. The case was about Google reimplementing Java API for use in the android davlik engine. That really isn't interoperability since Java wouldn't run on it. They just copied some java apis for the convenience of android programers.
Pardon my ignorance but is that really common in the programming world? To take someones API and use it for a totally different purpose?