Different database designs, but similar document model. In fact, Couchbase Sync Gateway is capable of syncing between Couchbase Server and Apache CouchDB. Also our iOS, Android, and .NET libraries can sync with CouchDB and PouchDB. Everything open source, of course. More info: http://developer.couchbase.com/mobile/
It's that these are fundamentally very different databases with different trade offs. You can't just take one and adjust some API calls and expect things to work in a similar way. It only confuses people when it's quietly ignored and others assume that since it wasn't pointed out to be wrong that it must be the same thing.
I've had far too many conversations with people who use Couchbase that can't tell the difference that I would say that it's just general confusion. It's lax work on Couchbase's part and a thorn in the Apache CouchDB project that there is no effort to help clarify the fact that they are indeed independent and now very different databases.
