The final piece was to alter the Add Panel action so that it was aware of templates. This means that you now get this when you right click:
That "Default Panel" entry does what you'd expect it to, and whenever we (or our downstreams) change what the default panel layout is then it changes, too, because both the init script and the context menu action trigger the same layout.
This also means you can create your own customized layouts. Which means one could even implement a "save this panel as a template" feature. It would also be feasible to add a "close this panel, but save it for easy restoration later" without too much effort. We could even GetHotNewStuff those panel layouts. We could provide the same functionality in the upcoming Activity Switcher for the desktop layer. Some of these "could"s will likely happen for 4.5, though I'm not sure exactly which ones yet as I'm now off to making the desktop toolbox a little less craptastic, as it's up next on the "to polish" rotation.