> Activating the degraded array is done only if the root fs is not
found,

Right, its only in a failure hook, and things like cryptsetup won't be run 
after that...
The initramfs boot mechanism is just not designed with the right event driven 
approach yet. Bug #488317


> and only if the mdadm package was configured via debconf to do so.

Not quite right. That debconf question was a rather bogus, unhelpfull an
unnecessary implementation. Bug #539597

> There is nothing wrong with this per se,

It is wrong to to use "mdadm --assemble --scan --run", because it will
start *all* arrays that have not come up yet in initramfs stage. (They
get desynced and need to be resynced) Bug #497186

-- 
booting out of sync RAID1 array fails with ext3 (comes up as already in sync)
https://bugs.launchpad.net/bugs/557429
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