The Unchained versions of Rogue Talents offer slight bonuses over the original versions of those same talents. In this instance, both versions of Surprise Attack grant you the ability to treat all targets as flat-footed during the surprise round, but the Unchained version adds damage to your Sneak Attacks as well.
Given that the additional effects of other unchained talents are quite minor, I would rule that the +5 is added to the total damage, and not to each individual roll.
The Unchained versions of Camouflage and Esoteric Scholar simply removes the "once a day" restriction.
The Unchained version of Combat Swipe allows you to qualify for the feat Greater Steal (the original does not).
The Unchained version of Hold Breath doubles the number of rounds the Rogue can hold their breath rather than adding 2.