You can count it only once for tier-ing up, though you can play each of three versions for their respective rewards.
Since Keith chimed in, here's an ongoing question from my group, STORY DESIGN wise, where does this adventure slot in? We feel its after 4-1, but trying to figure out story wise if it happens before, during or after 4-2.
Intent was before 4-2. That said, in terms of your journey, before or after both make reasonable sense.
In the middle of would be weird story-wise. Basically, both 4-P1 and 4-2 are in ports, but bouncing in and out of 4-2's while hot on the trail of something would be mighty strange :)
Thanks! We are gonna hit these while some of our group is in Maui in their own port adventures before 4-2 drops for us!