One requirement for AutoTune is that the PIDs you are using during AutoTune do not oscillate (or even "ring" badly).
If you tune a quad, then add a camera, it is heavier and will oscillate.
You can do it the other way around just fine: If you successfully tune it with a camera, then remove the camera, it does not oscillate, and you can use those PIDs to run AT again.
I know that recently I discussed using PID banks so you could have one tune for camera and one tune for no camera. I should have made it more clear then...