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I for the most part agree with the comments and will provide an updated patch on thursday. Would you mind if I committed that without further review (due to cutting it awfully close to the deadline for beta 1)?
Some comments I want to reply to specifically:
* "Can the code be simpler, with only one pass?"
 Maybe, but not right now. 
* "This is inconsistent with _flatten()."
 I'll add a comment that explains why this is: _flatten (and this code) 
 can deal with arbitrary keys, but that is not supported by Apple's code.
 The type check in _write_object ensures that it is not possible to write
 archives that cannot be read back by Apple's Cocoa frameworks.
* "unusual indentation" (several times)
 I'll have to look at other stdlib code to find suitable indentation, this
 is indentation I've used in my code for a long time (I've also used 
 camelCase instead of pep8_style names for methods for a long time, which 
 is probably why I never noticed that I forgot to convert some method 
 name when cleaning up the naming conventions used in this module).