TAnner's Setting details.

so my explanation is that none of the andromeda aliens are in the omnitrix because they're outside of the milky way galaxy, Alien X isn't in there because they mainly exist outside of the universe at the time of the dna gathering, Atomix's species were wiped out in an intergalactic war between them and the incurseans where the incurseans won via the help of a rogue Atomix who's remained well-hidden enough that azmuth wasn't able to get a hold of his DNA, Way Bigs are FAR rarer than they are in the other universes so they're pretty much considered a mythical legend to the point where azmuth just doesn't believe they exist so no DNA from them and Clockwork's species are far more reclusive than they usually are and guard their secrets closely via their powers so azmuth wasn't able to get their DNA either.