Potential solution:

Make the initramfs scripts completely ignore anything that is not
critical for mounting the rootfs and booting the system. It should not
even bother with /dev/md3 as it is not associated wih any aspects for
successfully come to a login prompt.
In this case, only initializing raids required for the successful boot
would suffice. Then it would assemble the crypt devices and hand the
system over to the init. Which would assemble the rest of the raids
successfully and then the rest of the encrypted devices.

This is basically what happens in 11.04.

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https://bugs.launchpad.net/bugs/1062159

Title:
  Raid is incorrectly determined as DEGRADED preventing boot in 12.04

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