Links between and within FT3 documents can be created by drag and ctrl-drop.
Here is a Keyboard Maestro macro for copying ft3doc:// links from other applications back to a particular chapter and verse in an FT3 file.
(it simply uses Atom > Edit > Copy Path to get a file:// URL, and then replaces the file: prefix (in the clipboard) with ft3doc:
( ft3doc:// links require the installation of a very simple helper script – details in the repository )