Historically yes. More recently there are fewer and fewer differences as stock/standard track bikes get to be a bit more neutral.
Sprint bikes will have steeper geometry - which means 75deg seattubes and headtubes or thereabouts. There was a trend toward very tight clearances in, oh, the 70s, that persists, though it's not super necessary.
There are good reasons for making madison and points race bikes differently. Riders will be on them for more than just a few minutes, so it makes sense to pull the angles down to 73.5, and set them up differently, too - saddles a bit further back, different bars at a different height. It lets the rider get a more comfortable position, the bike will be somewhat more stable, etc.
Obviously pursuit bikes will be very different, but what I've seen is some companies making a bike that can double as a pursuit or kilo bike AND an all-around mass start bike. They keep the head tube short and the top tube low, which lets the riders get as low as they want to on aerobars, and then the riders use a riser stem to put drop bars where they want them.