You seem to be completely on top of the issues and I don't have a magical solution for you... You didn't mention booking the IB flights as a BA/AY codeshare, but that's presumably something else to avoid if you want to guarantee your EQMs.

I know that people have long since stopped using actual travel agents to book flights, especially since they must charge a fee to cover the fact that the airlines now pay little to no commission. But your situation sounds exactly what a TA would be perfect for. There are many freelancing TAs who could do exactly what you require. For example, Propeller Travel is very popular with BA Tier Point runners and the fees are quite reasonable IMO...