I was helpfully contacted by someone from BA after this post who passed the issue internally for further research. Unfortunately, it looks like something was lost in translation.
After a week I got a note that they were asking AA for the Avios that I should have got from flying the route, so I responded as politely as I could explaining that they must have been given an incorrect summary of the issue. This was acknowledged in a follow up email.
Two weeks have passed since then and I haven't heard anything else. I thought that I'd call BA customer support for an update, but apparently the only people who can read the customer service system are only available from 6-9am PDT.
Will try to make some early morning phone calls later this week.