The mutually exclusive arguments are displayed with in the argument group, at least in my testing.  From a copy-n-paste of your example:

In [8]: parser.print_help()
usage: ipython3 [-h]
                [--from-args FROM_ARGS | --from-files FROM_FILES | --from-stdin FROM_STDIN]
                [-0 0]

optional arguments:
  -h, --help            show this help message and exit

INPUT OPTIONS:
  --from-args FROM_ARGS
  --from-files FROM_FILES
  --from-stdin FROM_STDIN
  -0 0                  null delimited pathnames


I've had occasion to note that this is the only kind of group nesting that works (or makes sense).

In add_container_actions, there is a comment:

        # add container's mutually exclusive groups
        # NOTE: if add_mutually_exclusive_group ever gains title= and
        # description= then this code will need to be expanded as above

So the original developer envisioned giving a mutually exclusive group a formatting role, but with this nesting this isn't needed (that I can tell).  But I don't think this has been documented.