So granted, I haven't ran exhaustive tests because I don't feel like blowing hundreds of gems testing it out. But the new "Auto Challenge" feature in Boss War does not appear to be working properly - it's consistently returning lower damage results than manually running through each individual fight on 4x Auto.
I ran my first Boss War this week on 4x auto. I got 15.2M. The rest of the week, I kept using Auto Challenge and kept getting results around 14.1-14.4M - approximately 6-8% lower. So I decided to run it again on 4x Auto...and lo and behold, I got 15.2M again. Then I reset and tried Auto Challenge again...and right back to the ~14.2M range. So to summarize...
4x Auto: ~15.2M
Auto Challenge: ~14.1-14.4M
Auto Challenge appears to be consistently returning lower damage outputs than 4x Auto.