The entire morning is a definite downside to this. I suspect a lot of people book the pirate cruise trying to fit in 'everything' - you aren't going to fit in everything at Disney unless you stay a month so you have to choose. The cruise is a nice thing to choose, but by the time you do activities like the pirate cruise, book a sit down ADR every day on the dining plan, get your kids to a waterpark, spend an afternoon at DTD, get in BBB, make sure to get your kid in the front row early for Jedi training - I wonder how people find time to ride BTMRR. (We've always told our repeaters to hang back - but they've gotten off the boat saying 'the other kids who knew where stuff was weren't waiting - why did you make us wait!' - so I suspect that isn't an uncommon issue).
jockey - they give you a pager, but its in case there is an emergency. The kids have two hours to finish a script that takes two hours. They can't take time from the other kids because one kid wants to go back to Mom - nor do they have the staff ratio to dedicate to that sort of 'emergency.' If you think separation is going to be an issue, this is a bad choice of activities.