It seems like you could be at the park right when it opens and still end up with a 60+ minute wait for Flight of Passage. I think there are around 30,000 rooms at WDW resorts. Let's say 5,000 are empty on any given day and that there are only 2 people in each room (my guess is that the average number of guests per room is higher than 2, but just for argument's sake). That leaves 50,000 people with the on-site perk. Let's say 10,000 don't take advantage of it, and the other 40,000 split between all four parks equally (which would never happen -- the Magic Kingdom will likely get the most every day, but again, for argument's sake). So you've got 10,000 people headed early to Animal Kingdom.
Let's cut that in half and make it only 5,000 people because some arrived a bit late or any number of other reasons. Now let's cut that in half again -- assuming some people go to Everest or Kiliminjaro (will that even be open early?) or wherever else -- so you're down to 2,500 people headed to Flight of Passage at open. Flight of Passage only has a 1500 person hourly capacity. Some of those 2500 people are going to end up at the back of the line and still have to wait an hour to ride.
I guess it's not an issue because the same thing could/should have happened with the old EMH, but you never really hear anyone complaining about that so I guess it didn't? I don't really understand how, though, given the simple math involved.
It's still an advantage over off-site guests who can't do it at all, of course.