You could pretty much say that about many rides making sense though? What's the 'story' with Pirates (before or after Captain Jack Sparrow was added) and how does it make 'sense'?
We're out at sea and suddenly go down a slope where there's a big pirate ship (how did the ship get there if there's a drop from the sea into the dock?) firing at a town containing more pirates? We see pirates causing mayhem and at the end some pirates locked up and a pirate not locked up with all the treasure. So are we being taught that it's ok to be a pirate and rob and steal as long as you're good at it, or is it a set of scenes to enjoy without thinking everything through too much?
How about Peter Pan if we'd not seen the film, would the scenes all make perfect sense?
We're flying over London and approaching a tropical island. There's some children, mermaids, pirates and Indians there, why? How did the kids get there, why is one walking the plank and why are there Indians there? There's a boy in green who's subdued the pirates and captured the ship, how did he do this? A pirate is standing on an alligator's jaw, how did that happen?
I could go through other attractions too but you get the idea. Some are better than others at telling a story, but a ride only has so much time to tell a 'story'. A lot of the time the visuals and the effects are what make the ride, if we want to find fault to the extreme of the lyrics not matching exactly what's happening then we could rubbish any attraction ever built.
For me Frozen would have probably been a better fit in the MK or DHS, however Maelstrom was something I rode only as long as the wait was only 10 mins or less. I believe the Frozen attraction is a far better 'ride' than Maelstrom was, far more entertaining and fun. I used to really hate the show you were encouraged to watch following Maelstrom, I'm sad to admit I used to run if the doors were still open to avoid it. Eventually they kept the doors open so it was optional, but I seem to remember originally they kept you in an area after disembarking and 'made' you all watch it?