They don't need your fingerprints, so they don't take them. I don't know about this "bone scan" claim exactly...sounds like a random CM "dismissal" quote.
But as already explained, it is not a full fingerprint scan - that would have so many issues that it would take forever to get through the turnstiles. Think of it as a very low res picture - you can kinda tell something is there, but you don't know if it is your uncle or an empty chair. But you CAN pick some distinctive points on that image, and translate that into some numbers, and compare the numbers fairly accurately to a previous image. However, there is still a chance it could think that empty chair is your uncle.
With the 1:1000 duplication rate, it certainly couldn't be used to identify you positively. However, there are many other ways that you probably don't think of that could be in use that does...
As far as the old way, I didn't think the "two-finger salute" was any better - in fact, it was slower.