That's a non sequitur. A society advances on numerous axis, but doesn't necessarily advance at the same time. Society can be immoral and enough scientifically advanced to have such machines. I'm pretty sure Romulans in that universe had replicators and they were known for their black ops division.

Good point. Though I think that the suggestion was that the technology required to materialise a massive, warp capable star ship may be more advanced than a different technology that accomplishes the same tasks as a star ship. For example being able to teleport both people and nuclear weapons across the whole universe would pretty much render star ships obsolete.

Maybe people are just too romantic and nostalgic to realize their wildest dreams with holo decks, telepresence, brain implants and let AIs decide on their well being. Maybe instead of spawning self-replicating robots for space exploration they want to do it physically themselves like their ancestors explored the continents a long time ago.

A human level AI could kidnap you, put you into a simulation like that and you wouldn't know.

Depending on what morality we put into the AIs it may choose to do so.