It might be helpful to add the capacity for custom content in the header without manually editing the theme, i.e. so content can be inserted into the theme header with the database.js file.
Context: I add a favicon to my site. Upon updating, I expect the theme php file to be overwritten and thus my manual changes would be lost.
I might even consider writing a plugin to enable easy favicon selection from uploaded files, but right now it doesn't seem possible to arbitrarily insert code into the header.