In PvP your using somewhat of a dumbed down Rotation. Like your using your Spammable, Single target Dot's, CC's and Executes but usually not your AoE Dot's (like Endless Hail, Blockade, etc.). That means your losing out on on the greatest part of the damage your character is able to deal since your not using some abilities.
And the second thing is your not necessarily keeping your damage against players up all the time or your using abilities that are doing lower damage but provide some utility like stun or closing gaps.
Since that is the case it is preferably to use sets that give you damage that procs instead of using sets that boost the damage of the abilities your using
However even that is not necessarily the case sets like ravager or fury can outperform viper damage wise in PvP if the player cares about keeping up Dot's.
It's not that sets like viper have absolutely no application in PvE (someone used Viper in Vma with great success), however compared to other sets that give raw stats they are significantly underperforming in terms of damage.
There are however other Proc sets that deal more damage than for example viper that are used for PvE but are highly impractical in PvP like Ilambris or Kra'ghs.