No, You won't encounter Sectoid Commanders and Outsiders in the end game, they are replaced on their post of "commanding aliens" by Ethereals.
But you have already researched them, as there is no way to reach Gollop Chamber without it. A "live" Outsider is an Outsider Shard that you need to locate the Alien Base. And Sectiod Commander interrogation provides you with Psi technology.