Hmmm, I seem to have somewhat figured out what's going on.
Using Marc's example, when you instantiate u it's doctype field is set
to the default for Documents (None), since it isn't passed in. Then
when you save it, it overwrites the field in d.
So it seems the answer to my question is something like:
d = Document(doctype='whatever')
d.save()
u_kwargs = <dictionary of the fields of d>
u_kwargs.update({
'document_ptr_id': d,
'filename': 'rat.doc',
})
u = UploadedFile(**u_kwargs)
u.save()
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