matchboxbananasynergy
I reset cache and storage, set an alarm with the default sound, and restarted. That worked. Then I set an alarm using a MIDI file as the sound and restarted. That showed just the animation with no sound. Then I went back to the default alarm, restarted, and that played. Then I set an alarm with the MIDI file, restarted, and unlocked -- that played. So my claim was too strong: it seems to be only non-built-in alarms that don't play BFU. I guess that could make sense, but if there is still fallback code in Clock it doesn't seem to be working.
With respect to permissions, I don't think I have ever revoked anything from Clock. The current state is:
Allowed: Notifications, Sensors
Not allowed: Music and audio, Photos and videos
Is that as it should be?