For my own count I DON'T count the guy who played Kloog who WAS billed, because clearly he was a stunt guy with no lines.
But since he was billed, then no, he was not an extra. "Extra" is not a matter of opinion. It's a professional job title with a formal definition, and it's dictated by the contract you sign and your professional standing. Someone who is contracted as an extra is an extra; someone who is contracted as an actor is an actor, even without lines. (And the SAG has a separate category for Background Performers.)
Perhaps the difference is that both Gem and Kloog were named characters who had significant interaction with other characters, even if they didn't speak. That put them in a different category from some anonymous Morg who jumps on Kirk's back or some yeoman serving coffee in the background. It may also be a function of duration -- how much screen time and attention the performer gets, even without dialogue. I've seen other instances where a performer with no lines was still credited because of the featured nature of their role. For instance, Carel Struycken as Lurch in the Addams Family
There can also be instances where someone is cast in a speaking part but all their lines are cut out. In that case, they still get the same billing and payment they were contracted for. Heck, there's a West Wing
episode that bills Armin Shimerman prominently in the guest credits even though he was cut out of the episode completely.
I think the rule was, a stunt guy who doubles for another actor during a fight or whatever DOES NOT get credit, BUT if he plays the person thruout the episode and is NOT replaced during the fight he sometimes gets billed.
But Mickey Morton (Kloog) is not a stuntman, but an actor. He has dozens of acting credits on IMDb
both before and after "Triskelion," and no stunt performer credits. (Hey, he played Chewbacca's wife in The Star Wars Holiday Special
!) Sure, he was generally cast as big, thuggish guys or creatures, often without dialogue, but he wasn't a stuntman. I guess you'd call him a bit player.