I believe the lore at the time implied that the cybernetic enemies (cyberdemon, spider, aracnotrons, mancubi, revenants) were the results of secret UAC experiments - the realisation being that the company have been 'working' with the aliens/demons for some time before the invasion. That there was a Betruger character in charge of betraying humanity and was working with the enemy, before they used our own technology against us (including teleportation tech). Makes them extra evil when you think of them that way.
One of the few good ideas in the Doom novel was the idea that the enemy force created its' soldiers in accordance with Earth's Christian view of hell and demons - meaning they 'designed' the Baron Of Hell to look like the stereotypical image of the Devil (and like, cloned them or whatever). That can also work with the caco (that Lovecraftian picture they were based on IRL) and the imp (brown pointy monster, boogieman or something). Don't know what the demons could be based on but c'mon, it's an awesome design for a creature.
And I've said this before, but the zombies are UAC workers/soldiers that have been 'zombiefied' by the Arch-Viles, I think - it fits with their attack (they can lock eyes with you and send you insane within seconds, unless they consider you too dangerous and light you on fire and blow you up Scanners-style instead) and can fit with the fact that there's none in Doom I - a whole bunch of them moved through the Phobos and Deimos bases, brainwashing all the staff as they went on their way....to EARTH...
So yeah, that's the way it went down.