Must've been the angle and lighting cuz now the new one looks smaller.
If the only real difference is the smallest diameter portion at the tip of the pin being longer, then this is insignificant. It'll just stick out of the hole in the caliper that much more. The portion following that is what actually locates the caliper and is where the caliper slides. That's the part I'd be concerned about. Screw one in at the top or bottom hole of the bracket and one of the originals in the other hole without the caliper in place and see how they compare. If the new one fully seats just the same as the original, then you should be good to go. The rubber boots don't have to be replaced it they're not worn or damaged.