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Developers of applications have the choice of using the system-wide frameworks, or their own copy built-in to the application. The recent Safari update changes the system-wide WebKit framework which is used by multiple applications to do HTML rendering, so that's why the reboot happens(*). If you use an OmniWeb sneaky peek or a WebKit nightly build, you'll be using the copy of the WebKit framework inside that application (use ctrl-click or right-click on the app, then select Show Package Contents from the resulting menu to see all the stuff lurking under the surface). Without the ability to use a private copy of a framework like this, development and testing would be (more of) a real PITA!

(*) I'm not 100% convinced that a reboot is truly necessary, as opposed to restarting all applications that use the affected frameworks, but using the big hammer does eliminate any uncertainty about whether or not everyone is using the correct version!