bcgallacher,
We have to assume that we have talked with the decision makers in the US, and LM, and established that the risk of F35B being cancelled is sufficiently small as to be outweighed by other considerations. Even so, it's highly unlikely they were reassured that it would a completely risk-free option. By going cats & trap, we had more fall-backs, as well as more inter-operability with allies.
If B should fall over, then we would be in a big hole from which I doubt UK fixed-wing carrier operation would escape. But it is the executives' job to make these hard calls (and they are hard, likely harder still when you have more knowledge than is available to most on here), and they have made their call.