(My first try with the ComboMod)
Those Spec-Ops guys are really nasty in the first missions when your squad is poorly armed and - most important - just veeery sloooow.
After a few weapon collections and speed upgrades, the Spec-Ops don't seem that impressive any more (I still don't know whether they get big guns and rocket launchers later in the game). So I got pleased to see them.
I've met Spec-Ops in several missions, once even inside a base (but then the game crashed and when I reloaded I got transgenants instead
There seem to be only one "golden" rule: never had a mix of Spec-Ops and transgenants in the same mission. I think the idea is that Spec-Ops could get complexed when put together with the better-looking and more handsome transgenants
Or: the transgenants eat people including Spec-Ops. In fact, most transgenants use different parts of human bodies but none seem to assimilate brains. This could explain the inability to distinguish friend and foe humans. Or maybe this is just as stupid as it seems...
By the way, I never got poorly-armed rebels. Which is sad because I like the sound of the "poorly-armed" part.