Excellent survey of the landscape and definitely some invaluable suggestions. Personally, I prefer to scatter documentation where it's needed rather than compiling it in one place. My custom themes typically use Advanced Custom Fields which allows admins to place instructions on a field or even add a message field. My experience has been that placing such contextual help in front of the user/client is more likely to curtail common questions than if they continually need to refer back to a central source each time they have a question.