I do have bind mounts, and I described these in Some DNS settings being lost on docker restart - should have repeated it here, but I had abandoned hope on that item 
Every other setting is persisted, all other content is saved between restarts.
I've never shared my configuration - I've started each one from scratch and allowed docker to create the paths. In all cases (docker on Mac, docker on Linux bare metal, docker on Linux KVM guest), the same behaviour occurs - all settings OTHER than these two are persisted and these are lost on each restart.
So I've given up trying to fix the underlying problem, and just want to manually set these now which I think yubiuser has kindly answered.