In my opinion it is not only correct assumption that they should behave identically. They should behave predictably. Practically all machines are individuals. Manufacturers give certain acceptable range for performance and other properties. Of course most virtual worlds behave more perfect way, but it is weakness of them and not strength.
Yes, unfortunately this is true. But I still hope that at some day someone (maybe artificial intelligence if humans are too greedy for it) will make interesting game for engineers which do not try to be easy to begin or have beautiful graphics, but instead have complex and interesting mechanics and room for planning. Factorio would be very good starting point for such a game. I mean something like Orbiter is in space games.Then Factorio will lose half of its audience.