In terms of speculating, such as "More logically, that would indicate such beings are related to this biosphere and descend somehow in the broader genome of the Earth..." one could also, reasonably and logically, assume Earth was seeded for the direct purposes of harvesting produce.

While entertaining the theme presented, which I am not opposed to, I considered a variation of the Morlocks, as presented in HG Wells, the Time Machine. Another proposition for those underground, machine operating mutant, descendants of humans is that they're actually the remnants of the reptilian civilization that survived the 'great extinction.' If humans survived a nuclear war, but not cattle- well, guess who's coming to dinner?

There are so many ways to be invisible, I don't understand why science isn't interested in this.