I think we're missing the point. What if Busch Gardens is really the front for an illegal Government Bald Eagle cloning facility? It would have to be secret since cloning would piss off the people who think the eradication of a species is "God's Will" and cloning would circumvent that. They were endangered and were recently removed from that list, the park could be responsible about that. The location makes sense as well. It has to be away from large cities since,
"The Bald Eagle is usually quite sensitive to human activity while nesting, and is found most commonly in areas with minimal human disturbance. It chooses sites more than 1.2 km (0.75 mi) from low-density human disturbance and more than 1.8 km (1.1 mi) from medium- to high-density human disturbance."
(Source)
That's why you can't have an Eagle cloning facility near large human populations and why they're not commonly seen as often as say, squirrels. It would also make sense since the eagles that can't fly are the park's clone rejects.