Hello,
I have read about difference between certified and signed PDF document here:
http://www.geotrust.com/signing-products/document-signing/individual/f aq.html#7
and I understand (+--) it.
The "certifying usage" is IMHO proprietary Adobe thing and Certification Authority do nothing to do with it (key usage in certificate).
Certificate is published for signing and knows nothig about such differences in special case of PDF documents.
Of course, I could manualy set in Reader certificate as trusted for certifying, but it is insecure/unofficial solution.
Thanks --kapetr