I agree. Using API key to determine what kind of information is returned is a strange solution. It would effectively mean that if the airline is developing an application that has multiple levels of users (airline employees, customers, admins) it would need to store and use multiple API keys to retrieve the data.
Ofcourse, real solution here is that the airline software should not just pass along everything it received from Amadeus but rather that they should convert it and return only the relevant subset. This would avoid these type of issues.