I spoke to a couple of our PS folks, and here's the gist of what they said...
The new 6.x feature, the static asset manager (the “Manage Files” button in HTML and Formatted text widgets now) will be enabled in 22.214.171.124. This would be a the ideal place to store because you can change the Email Template header via the Admin Console (stored in DB) and have the asset that is being reference stored in the DB as well. Until you get to 6.0.1 there is, unfortunately, no *good* way to do this.
Thanks for getting back to me. Well, I don't love it, but is what it is.
Now that we are up to 6.0.3, has anything been implemented that's more intuitive than this workaround?