I agree we have probably been a little overzealous in this case.
We released 1.5.4 to the beta store yesterday which limits the number of buttons which has this protection down to the ‘confirmation’ buttons only - so send money and confirm top up. This no longer affects the FAB or anything else. We also show a message now to explain to the user that they have an overlay in use, if they try and use those few buttons with the overlay.
Our intention is certainly not to annoy our users nor block apps like Twilight, it’s just an unfortunate side effect of adding this measure.