The article that you link to does not relate to CloudKit, and in fact
does not even mention CloudKit. CloudKit is not iCloud.
What the article says (which is probably true) is that apps distributed
outside the app store can access iCloud Drive. This is a new feature yet to
be officially released which will apparently be something like Dropbox.
Apps will probably be able to read/write files in iCloud Drive just like in
any other folder on a Mac.
CloudKit is an entirely separate system with a web service-style API for
reading and writing structured data using Apple's servers. It's not
available to apps outside of the app store, because those APIs won't work
unless the app has the appropriate capabilities via Apple's app