The docs are silent on this questios. Will the commands be registered in order, with later apps (in settings.INSTALLED_APPS order) overriding previous commands (whether custom from other apps or the built-in Django commands)?
The answer is yes, as of the current 1.7 release.
See this line in the Django source to see where the logic is implemented: in the order of apps per the settings.INSTALLED_APPS tuple, each app's management commands are added to a dictionary of commands (which was initialized with Django's built-in commands here), with a single slot for any given command name, so that last one added sticks, overriding any previous app's (or Django's built-in) command with the same name; when executing a command (code here), Django uses the dictionary above to decide which command logic to actually use.
Note I haven't found any documentation of this, so it should technically be considered unofficial behavior.