It sounds like it goes both ways, so to speak. I spoke to my travel agents some more on this issue and one point they raised is that there is less paperwork to process a Type A than a Type B. So allowing a certificate to be used either way is advantageous to both the passenger and agent.
Our agency has gotten tickets rejected by the ARC so they are reluctant to process many of these vouchers. There does not appear to be a clear policy on what can be used with what on UA, at least. They recommend using the CTO in particular for combinations of discounts and vouchers.
Charles