Regarding engines: A random tidbit I picked up about nuclear submarines is that the reactors actually require quite a bit of manual tuning and observation. This was intentional: especially back in the day of the first nuclear subs, automation hardware would have been bulky and (spacewise) expensive, and the alternative was to leave the systems manually-tuned and train sailors to do the job. From a safety perspective, one of course chooses automation... But war has a different safety perspective, and the great thing about a sailor is that when they aren't busy running the reactor they can do something else. They can also react to a captain's needs and get creative in a way that an automated system can't (a major concern for the design was that a captain could be hamstrung in a sea battle trying to get the sub to do something that the safety interlocks disallowed).
That aspect of real vessels, that it's possible to "redline" them and run them in a configuration that is temporarily viable but risks damage or makes them more vulnerable in some other way, is an interesting piece to play with in a game environment as a risk players can choose to take.
So if you have fewer players, you can play on a smaller ship that doesn't have any non-player crew members. Or, conversely, a large group will have additional stations to spread the work out a little bit.
Hopefully everything feels meaningful and impactful at every crew and ship size and nothing feels like busywork.
The goal for Thorium Nova is to create that iron-clad simulator that you're looking for, where every crew member's job has a real impact on the overall simulation. Right now I'm working on the power grid simulation, which will have huge effects on the rest of the ship. The quartermaster will have to keep fuel and coolant stocked in the reactor room, the engineer will have to monitor the reactor's usage and heat to make sure there's enough capacity for an emergency, and someone else will be in charge of answering the captain's call to "reroute all power to the engines!"
Building these simulations is an interesting balance of realism and gameplay enjoyment. Hopefully I get each of those right.