My friend figured out a fix:
Create a new scheme for the base app (not the extension)
Build and run that scheme (it'll show an error dialog and not do anything)
You should now be able to run the extension as expected
This seems like an actual bug with the project template so I'd be happy to elevate this ticket if possible.
noahbkim
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It seems like changes to the extension won't be propagated to the test device/simulator unless you rerun the main app target. I figure this means the MessagesExtension scheme is bugged?