There's nothing to prevent multiple services from using the same port at this stage. For files in /etc, the "etc" service should detect that the same file appears more than once and error out--that is, it won't instantiate a "broken" system.

There are other things that are detected statically and prevent you from instantiating a broken system: missing modules in the initrd, invalid file system label/UUID, references to non-existent Shepherd services, etc. All this is possible because there are well-defined data types and semantics for the different components of the system.