Its my understanding that Meteion was gathering souls there as a source for her dynamis and when we arrive its Thancred's will bending the dynamis to create everything there. The question becomes, how accurate, how thorough, was everything recreated? Ysthola warns us that these are effectively illusions, souls with no aether, but that doesn't make them less real; get in a fight with one and it will hurt you. By a similar token, we have the soul of Sir, and possibly a great many of the race, but do we have all of them? The Omicrons spanned multiple worlds and while they are sentient, are all machines on their world sentient? Are their factories sentient? Its shown during the MSQ that things were created well enough to mimic electricity and wireless communication. My interpretation was that regardless if the soul of Sigma was there, we were sending a communication to somewhere else to change what the factories were doing on some far away planet. If we hadn't, then eventually we'd have a horde of drone missiles coming towards Etheirys.
As for the cafe...the lopporits didn't get the memo that these things aren't real so they're treating them like a new race they've met. And its probably a set up for the beast tribe quests later.