Depends, really. Generally, it only fades for that person. Others are still affected normally.
Hell, in 3e there're options to make [shadow] spells more real if you succeed at your saving throw against them and get hit harder by such spells as a result. Really nasty against tougher enemies, and it's totally an option that Alchemist & Co have at their disposal.
I think Fate has a True Seeing or similar effect, allowing him to see through the illusion of realness. Nobody else there did (and literally everyone else [barring maybe Wonder Woman] failed their saves). If he'd been there at the summoning, he would've seen that it was a real, bona fide, Capital-G Creator God that got pulled in through Alchemist's Power of Bullshit Hax™.