I know that Xcode doesn't have explicit support in the UI for Package Registries, but can use packages referenced by ID if the registry is set up through the CLI.

I also see that xcodebuild has support for SCM to registry transformation (resolving and downloading packages through a registry, even if the packages are referenced using their Github URLs) through options like -defaultPackageRegistryURL and -packageDependencySCMToRegistryTransformation. Is there any way to achieve the same thing in Xcode itself?

Have you seen in the Xcode add package dialog, at the bottom of the sidebar, the plus button which offers "Add Package Collection"?

Package collections aren't registries.

Fair enough. Are they collections of collections, then?

Are you familiar with NPM, PyPI, or homebrew (sorta)? Registries are like that. Instead of having to clone the whole repo of the package you're pulling in, SPM can just download a zip file.

I filed FB14699700 asking Apple add this feature to Xcode to document it if it already exists.