To me, a lot of the FreeDooM monsters seem more like parasites

As if they're creatures powered by nuclear waste and other toxic chemicals. The pinky demon replacement for example, as well as the imps and such. Maybe even the former humans. Is this just me or does anyone else have this strange thought?

i've thought that too

I never really thought about, as they tend to be a bit too vague for me to guess the origions.
But sure, why not? Let the players think what they are and stick with it.

And why else would they mostly be in a tech themed area? A place where there is indeed a large amount of toxic waste? And maybe they were taken into Hell as backup forces.

We will never know, until the story/theme gets chosen.