Most skippers I've dealt with are happy enough to accept an aircraft with auto brake inop depending on destination runway and conditions of course.
I am not across our mobs directions in A/B use in day to day ops.
However in the old days when I could dispatch a 737 without any A/P I've had f/o's in particular happy as larry to actually fly it and one skipper nearly crapped himself at the prospect.
In the Boeing notes you quote , are they not saying you should use A/B under those conditions and not risk manual braking, not the inference that you should not use A/B under "normal" conditions as you suggest?