After some more attempts, I finally figured out how to get the md3 raid
set up the same way as partman does with md[0-2] on the Alternate
installer CD.  There have been some constant issues that I forgot to
mention that may be a factor.  Whenever I attempted to repartition sda
and set the partition type to FD, as soon as I exited cfdisk the dmraid
system would mount md3 forcing me to mdadm -S /dev/md3 so I could
repartition sdb.  In addition, /dev/sda1 wouldn't show up while
/dev/sdb1 did but fdisk -l would show it existed on sda.  mdadm didn't
see it so I'm not sure if fdisk was getting it out of /proc/partinfo or
just assuming it existed.  Without it I couldn't create md3 on sd[ab]1,
only sd[ab].  Thinking that was part of the problem I tried various ways
of getting sda1 to show up including partprobe, various dd zeroings, and
repartitioning.  I noticed while doing this that cfdisk doesn't set the
serial number in the superblock so I used mklabel in parted to set it on
both drives first.  Finally I repartitioned sdb as ntfs, zeroed the fist
0.5MiB or so of sda, removed the md3 entry from mdadm.conf, and
rebooted.  I then repartitioned sda as type FD and then sda1 showed up.
I then created md3 on sda1 without a second device and rebooted again to
make sure it was persistent.  I then repartitioned sdb and added sdb1 as
a hot-spare and let it resync.  After some more reboots and tests, I ran
pvcreate on md3 and checked the superblocks - they remained intact this
time.  I rebooted and double-checked everything then added md3 to vg0
and rebooted.  It failed and I ended up in initramfs busybox.  I removed
it from vg0 and was able to boot again.  So there definitely is a
problem with booting from a vg with multiple pv devices, at least if
they are md.  My workaround was to create a new volume group, vg1, that
only had md3 in it.  I lose some lvm flexibility this way but at least
it boots usually.  By "usually" I mean that there is an additional error
that now pops up every few boots:

device-mapper: table: 254:0: linear: dm-linear: Device lookup failed
device-mapper: ioctl: error adding target to table
Command failed: Not a block device
cryptsetup: cryptsetup failed, bad password or options?

I never get a LUKS passphrase prompt.  I can't unlock the volume from
initramfs either.  All I can do is reboot and try again.

I also noticed a suspicious error on the boot attempt immediately after 
removing md3 from vg0:
Starting kernel event manager...                                      [ OK ] 
 * Loading hardware drivers...
error receiving uevent message: No buffer space available

I found some references to an old kernel bug but this message only
showed up once so it may be unrelated.

-- 
pvcreate causing problems for dmraid
https://bugs.launchpad.net/bugs/183930
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