I'm not saying the story itself is totally illogical, I'm just saying the layout of the end of the attraction as it pertains to the story falls apart if one thinks too hard about it. Which, in fairness, we shouldn't be doing about either version. Here's what I mean:
We board the Jurassic Park River Adventure, an attraction in Jurassic Park, to see the dinosaurs. So we're imagining that we're on an attraction inside JP. But..
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As we can clearly see, as Guests, there is no other connection point to the Unload zone. What you and others are saying about the maintenance building is fine, I get why a boat could end up in there. But why is the only "out point" for the attraction, a building that we were never supposed to be in?
The entire ending of the original JP ride relies on the fact that we
didn't take the boat's intended course. Which means that course should exist, in some capacity,
somewhere in order for things to make total sense if one thinks about it. The yellow line above is an example of maybe where something like a faux track/exit could have been placed to create the illusion that there was another path we missed the entire time.
We see the faux path in Hadrosaur cove:
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But we don't have anything close to that for the end of the attraction when it was JP. JW addresses this issue by making that path the intended one the entire time, is all I'm trying to say. That's for better or worse, which is totally up to you.