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David, I'm not sure I agree with your theory.  At Jim
Fulton's request, when creating a subclass, Python actually
looks through the base classes for one that's not a regular
class, and gives that one control of the subclass creation
process. So MyDerivedClass really should be a Boost.Python
class!  (Lorien can easily verify that by printing
self.__class__.)

Otherwise, if it was a regular class, the __init__ call
woudln't have failed in the first place!

Since I don't have Boost (yet), I can't look into this
further right now, and I fear it will have to remain
unresolved until after the 2.1b2 release.  But I'll try to
look into it again before the final 2.1 release.