The flamingo thing isn't a good argument. Tons of zoos still keep them with clipped wings. Putting them in aviaries is best practiced but not required welfare. There is a stark difference.
As to your first point, there are obviously compromises that need to be made between gameplay and outright realism, but it's clear that Frontier cares about how flying animals are kept, otherwise there wouldn't be a Walkthrough Exhibit.
I haven't seen any spoonbills in zoos that I can remember (only royal spoonbills in the wild here in NZ), but I've seen plenty of ibises (northern bald and scarlet, and other species I believe but it's been a while), and I can remember them being perched on faux rock formations, branches, and so on, and hardly on the ground at all. Like most aviary birds they barely did much of anything either, mostly just hanging about (ideal behaviour for exhibit animals, incidentally).
In any event, the question isn't "do I want them in the game under these circumstances" it's "will Frontier add them" and IMO it's not very likely. They blur the line between what is acceptable as a habitat animal and an exhibit animal. So do koalas and sloths and they ended up going both ways and nobody was 100% satisfied with either. IMO if they plan on adding another habitat bird, it will be something far more clear-cut; rhea, crowned crane, another swan, another penguin even, possibly even another flamingo.