I would guess that you are right that they were originally made for the Bonny engine and they assumed all the egine/air box dimenssions were the same. I was at the dealer last week hoping to see a new R3 Touring (no luck) and took a couple minutes to compare bike models and what the intake port looked like. I notices that what I did see, all but the america and speedmaster had straight cut ports but the america and speedmaster had angle cut intake ports.
The billet intakes were cut square. I think I saw bonnies, thruxton and scrambler.
Gary