the built-in documentation sets appear differently depending on whether one is viewing them in Xcode or in a web browser, I think appledocs documentation should do the same.
In a web browser there is a large header at the top, as well as a table of contents on the left; whereas in Xcode the header is absent, and the table of contents is hidden in favor of the Xcode jump bar.
But with appledoc generated documentation it looks the same in both Xcode and safari, showing the web browser header and table of contents on the side, and does not take advantage of the jump bar.
This would require using different html template - either automatically when enabling doc set generation or via an explicit cmd line switch. Code change would be trivial, most of the work would go to updating html template.