Chocolate Television,
yes, that's pretty much exactly what I'm saying, but I may be talking b*ll*x as I have no experience of bike engines except simply looking at them.
Most bike engines are used because they are light, cheap and have a gearbox built in to the engine casing. It's possible that the gearing may be changeable, but given that many of the BEC builders are looking for 3.14 diffs, I would guess that it's not as easy to do as it is with, say, a Ford gearbox.
As for the V-twins, the ones I've seen generally have the forward cylinder inclined, but the rearmost is almost vertical, given that there isn't a great deal of clearance between the top of the Blackbird/Fireblade engines and the bonnet, I would think that a V-twin would struggle in this area.
Furthermore, using an inline 4 allows all the carbs/throttle bodies to be in the same plane and to use a common airbox, I would think that the plumbing for a V-twin might be more problematic.