The higher bottom bracket shouldn't mean that the frame is smaller but it does mean that top tube clearance is probably not the best test of size. It is the top tube length that is really critical for fit. There is some argument on these forums about whether the top tube of a track bike should be a couple inches shorter than a road bike or not.

http://www.sheldonbrown.com/frame-sizing.html

I have ridden a bike that is "too small" for me for the last 10 years. It shows a lot of seat post and it has 130mm stem but for me it has been perfect. Better too small than too big.