I think a development team needs to ask itself if the api is stable and has a stable team behind it. Example Java libraries. If so, use it. If it has a company like Google or a small open source team, then protect your self by isolating the use of the api. Create a library that maps from your own internal api to the outside api. Even if it is a direct one-to-one mapping, you have only one place to make changes if the outside api becomes an orphan.
I don't think "API" is used in the same sense as what you are using it in. The author is talking about not building your business around an API offered by external service provider (eg: Google Translate, or Twitter for example) where your business is dependent upon the the external party continuing to offer that API.
