Anthony Flynn was on the fifth day of his job as the new chief executive of Covenant House Texas when the nonprofit battling youth homelessness opened its new campus. He smiled as residents, ages 18 to 24, moved into the 104,000-square-foot facility, designed by the global architecture firm Gensler. It boasted magnificent views of mature live oaks and the downtown skyline; outdoor gardens and an indoor basketball court; a clinic, a dining hall…