A pinioned flamingo won´t ever injure itself on a roof of an aviary the same way a chained elephant won´t ever fall into a moat or attack another member of the herd. To "protect" an captive animal by restricting its basic freedom to move in a natural/physiological way is morally questionable at the best. The pinioned flamingo might injure itself during a stampede when the flock has been excited during courthip displays (it includes synchronised running of the flock at high speed) or frightened and trying to escape. Pinioned birds will still instinctivelly flap their wings to speed their run/take off and lose their balance and crash to other flamingos and fall to the ground, they never adjust. I´ve seen it many times. I´ve seen a pinioned flamingo get cought by the remains of its amputated wing in mud/branches near its nest and almost drawning. After I´ve called the keepers and they helped it, it was so covered in mud and exhausted it wasn´t able to stand on its feet. Would it happen at night, the reliable breeding female would be lost. I´ve also watched countless unsuccessfull mating attempts by pinioned males and I would describe their emotion in an anthropomorphic way as pure frustration.
Comparing the percentage of infertile eggs in pinioned and unpinioned flamingos suggests 2/3 of pinioned males are unable to reproduce. How can any institution that even remotelly cares about genetical health of captive populations agree to this procedure, when you even don´t know which males will be the lucky 1/3 that you can use for your future breeding? How can you allow to lose so much genetical variability in just one generation? Not to mention lesser flamingos where pinioning is one of the causes of a very low reproduction rate right now. The AZA studbook keeper mentioned all their chicks are only from pairs containing an unpinioned male. The pinioned flock of lessers at Zlin produced almost 10 eggs in last 2 years but all turned to be infertile, other collections show similar results. The last hope for Andean and James´ flamingos in european zoos is not WWT, but the small breeding unpinioned flock in an aviary at Berlin zoo.
As I´ve mentioned in some old thread, I keep tabs on the captive flamingo population in Czech and Slovak zoos, thanks to annual reports and visits. The figures show the mortality rate for adult flamingos in aviaries is 1/3 lower then for flocks kept pinioned in clasical enclosures. The number of reared chicks in aviaries is double of the chicks in open enclosures (the positive difference would be probably higher if part of the birds in aviaries wouldn´t still be old pinioned ones), even when the average breeding flock size in aviaries is slightly smaller.
To minimalize injuries of flamingos in aviaries, it needs carefull evaluation of dangers, terain and natural behaviour. By using soft nets, maybe lowering the aviary roof, minimalizing constructions/pillars/trees inside the aviary, clever usage of vegetation along the aviary walls etc. Or you can attempt to build an exhibit in Basel´s way, where surrounding large trees and vertical nets are able to "catch" flamingos who would try to take off.
When Dvur Kralove covered their flamingo exhibit (ca 1000 m2) with a simple aviary, the whole project and construction costs were less then 10.000 USD. In the age of elephant/ape/bear habitats costing tens of milions, why are zoos unwilling to invest a little bit into their flamingos too?