In bug 1512436 we got support for "built-in" extensions read directly from omni.ja. However, there is no current support for handling updates to these extensions (ie, when the application changes, noticing if the built-in extension has changed and needs to go through the extension update logic).
Built-in addons are currently only used for the default theme and builtin search engines which are simple enough (and change infrequently enough) that this has not been a problem. This is much more likely to become a problem if we ship full-blown extensions (e.g. screenshots) in this way.
I'm pretty sure we have to handle this within the addon manager -- the update check really needs to happen before we call startup() on builtin addons and that happens relatively early during application startup.