i would absolutely feel comfortable challenging him in a well-intentioned and non-disruptive manner. it's entirely possible i'd get shitcanned afterwards and if so, that's fine, it wouldn't've worked out anyways for me if that's the environment. i've personally never been afraid to challenge people above me on the org chart who have the ability to fire me with a snap of their fingers (again, in appropriate, non-grossly confrontational ways). it's generally worked out quite well for me and tends to gain me respect in the eyes of my superiors. successful people tend not to have great respect for sycophants.

the good news is that in this hypothetical i'd be skilled and talented enough to be working with john fucking carmack so i wouldn't exactly be concerned about my ability to find a new gig in about 3 days. that's my point. now if there were evidence he'd be liable to blackball me in some way (no evidence of that to my knowledge), then the power disparity argument has more legs in my opinion.