Yes, that's the question I have been pondering for the last couple of hours (maybe more). And I am begriming to believe that it cant be done. Other than for the route of either writing a feature receiver to upload the template to a list on activation (but I think this approach is unclean) or modify onet.xml (a site definition?). I think both approaches are unnecessarily complex for the task at hand.
Think about it, just so that I could have a custom document library or form library with a custom document template I would either have to write code or modify the site definition. Isn?t that a bit unclean? Why cant it be done as a feature?