Normally you only need the “Allow app extension API only” for extension targets, to get warned if you are accessing API which is not available for extensions. I had enabled it for a framework to make sure I didn’t call forbidden API.
I found this issue at the same time as this other issue because my client complained about both problems: Not seeing any documentation via Quick Help as well as the generated header unnecessarily containing internal classes. This problem was already present in Xcode 8, as evidenced by somebody asking about it on Stack Overflow.
Filed as rdar://34790796 and on Open Radar. The mentioned sample is on my Radar Samples GitHub repo, titled InterfaceTest.