Is it possible to register external methods for Zope using a configure.zcml file or something similar? I'm trying to register external Python scripts (similar to other registry items such as "jsregistry.xml" or "cssregistry.xml" in themes)
No. External Methods are "old tech", pre-dating the Zope Component Architecture by several years.
You can easily add a GenericSetup import step that creates ExternalMethod objects on demand, but since only python modules located in the Extensions directories (inside Products and the INSTANCE_HOME location, you may as well just enumerate those locations via the usual Python file-access methods, add everything you find there and not use a registry at all.
However, are you absolutely certain you want to use an ExternalMethod? Wouldn't a simple utility or view be easier?