Hi Craig,
The way this works is that the code behind the register patient app is an "app template", plus java and gsp that support different functionality based on the configuration. Different implementation can have different app definitions (which inherit from the app template), and an implementation can even define multiple registration apps within one OpenMRS installation, each with a different configuration. (E.g. at Mirebalais hospital we have an ED registration app that has the unidentified patient option turned on, and an everywhere-else registration that has it turned off.)
Whereas an implementation that doesn't want that can (either through code, or via the administrative UI we talked about earlier on the thread) disable that, and define their own desired app.
Basically, I think we'd want to introduce some functionality in the Manage Apps page so that, if you choose a specific app template, then instead of editing it via the generic (big textarea) screen, you get a custom screen for editing that kind of app. And we'd custom-write a single page for editing a Registration app.
Does that make some sense?
-Darius