I think I may need to re-think my position. I think these are more batteries suitable for beetles. Or if I use one for each system, do I still stand a chance of making the full 3 minutes?
I would say those batteries were too small. I use one in The Honey Badger 4.0, which a Beetleweight. I would think in a Featherweight, the draw on both would probably kill them within the three minutes but for testing, they should be OK for very short bursts. The 4200mAh battery pictured is a better fit but if you want two separate batteries, I'd probably go for anything upwards of 3000mAh in that setup.

I've played around with the mixing slightly to behave itself but I'm wondering if anyone knows of this being a continual issue or if I simply have a dodgy old TX.
If it is a Feathertwo Dual, I would turn off the mixing on the TX altogether as the two mixing can have some odd outcomes.