I gave a shot at adding an extension through a custom module for the header provided by App UI. So I'm talking about this extension point ID:
And from my trials, I don't think this is reliably possible because of this line:
Map<String, Object> configSettings = exts.size() > 0 ? exts.get(0).getExtensionParams() : null;
So App UI is picking the first extension config in the list of such extensions, and that's the one that is consumed by the view. From my quick trials it wasn't clear which one would be picked (the one from the Ref App module or the one from my custom module).
If you agree with my assessment, I could open a ticket for this so that it becomes based on a priority order or something along those lines.