I know what the projects are about: Safari is Apples browser. WebKit is the engine used in Safari (and in many other browsers) which is open source. The WebKit source code contains also code to compile it as a standalone application. You can download the nightly build of WebKit here: http://nightly.webkit.org/
I have compared some of those nightly builds of WebKit to the official Safari application. And besides the slightly different logo and the different name, I haven't really seen any difference.
Are there any? Or is it just the branding?
Edit: I just tried again with the current nightly build of today and it even names itself "Safari" now.