From my understanding the best in bags feature or the best in slot features is based around the talent build you input. As it shows you a percentage increase from your talent setup and your current(?) gear there is no clear way to tell which build would output the most damage.
In theory, you might achieve a better damage output build altogether with another talents and changing gear accordingly. This is typically so for enhancement shamans, where you can choose to go into restoration for Nature’s Guidance 3% hit / spellhit but offers no other direct damage bonuses, or if you don’t need the hit you can go deeper elemental which grants you damage bonus to both your melee and spell attacks.