1) Be very careful about saying someone's bike is too big or small based on what they post without a pic. I'm also 5'9" and ride a 56, and would ride a 58 before I'd ride a 54. Before you claim I'm riding a too big bike, I can't swing a chain without hitting an elite coach who would tell me exactly what was wrong with my position.
2) BB height really has nothing to do with what the cockpit size should be. You'll be higher off the ground, but once you're on the bike, standover is irrelevant. The distance between your various points of contact on the bike should be very close on your road and track bikes, with adjustments if you're primarily doing match sprints or pursuits. If you're riding mass starts it should be pretty close to the same.
3) Crank length depends on the track you ride and the style of riding you do. I ride 165s on a 46 degree track (and everywhere else, too). Lots of cat 1/2 racers here ride 170s, and I know of at least one guy who was riding 185s, but pretty much just for pursuits.
4) some of the races may be shorter, but mass start races can still be as long as a crit, and when you're training you might be spending hours on the track bike. It doesn't have to be quite as comfortable as the road bike, but it shouldn't be much different.