Can you encounter lower tier aliens in the late game?
Solution 1:
No, you won't encounter Sectoid Commanders and Outsiders in the end game, as they are replaced in their post of "commanding aliens" by Ethereals.
But you have already researched at least an Outsider, 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. Sectoid Commander interrogation provides you with Psi research credit, which is not required to reach the end game.
Solution 2:
My experiences differed a bit from OrcJMR's.
The Sectoid Commander's autopsy unlocked the Psionic Labs facility.
Interrogating the Sectoid Commander provided a psionic research credit.
You can also run into groups of Sectoid Commanders in later missions. I remember one particular mission I had against Ethereals and Sectoid Commanders in the smallest UFO type at the same time on iron man. However I do not have a screenshot to substantiate my claim :-/
Solution 3:
Just to consolidate the right answers into a single one (and I take litte credit for most of the content):
The only alien type that you will definitely not see again is the Outsider, as they are never seen after you do the base assault mission. However, you must have captured an Outsider to have progressed the story this far.
Sectoid Commanders have been replaced by Ethereals as UFO commanders, but still appear in groups on normal missions.
Sectoids are rare, but do sometimes crop up on normal missions in late game. Ditto for (non-heavy) Floaters.
Thin Men are plentiful if you can wait for a council special mission, and do sometimes appear in other missions too.
It's not spoilering anything to say that you have a good chance of meeting most of the above after activating the Gollop Chamber, but for reasons that would be spoilery I don't know whether captures after that point count towards the achievement :-)
Solution 4:
Sectoid commanders do appear in the very last mission where you take over the alien base. There's a bunch of standard sectoids, and also 1 or 2 sectoid commanders as well.