I have had success doing this over the phone despite the agent protesting otherwise. I booked using my CX number and then asked to have the BAEC number added. On MMB I can select seats for free and the booking shows the BA miles and tier points I will earn.
On a reward booking I called up and the agent who asked me what seats I wanted and selected them manually for me. However, these could not be changed without a fee until OLCI.