Why is "auto adjust brightness" washing out my retina display on El Capitan?
It is a new feature called ‘Ambient light compensation’. Before the Beta 7 or so it was a separate option in that menu on your screenshots, but in newer betas and in the finale release Apple merged it with the ‘Automatically adjust brightness’ checkbox, so yes, it is now adjusting not only backlight brightness, but gamma as well.

The only solution I found so far is to turn off that checkbox and adjust backlight brightness manually, which isn't a solution really. Hope Apple will bring back a separate checkbox for ambient light compensation.