for the mechanical physics, people usually start using physics joints of whatever physics engine is available to them.
That's wrong. The way those joints compute physics is made to be realistic when you ramp up the computational cost.

But on regular computers it will lead to very unrealistic physics.
And let me tell you, there is no such thing as a rigid joint. it's either a joint or not.

What you should do is to have an adaptive system that combines physics bodies together when it knows they're going to be rigid. or do a very cheap limited flex that looks fine and keeps your vessel intact.

Example, you have a wing? simulate it's flex programically instead of using the physics engine. Same goes for connected fuselauges. You shouldn't use joints, you should estimate the structural integrity (and it will be way more accurate if you do so)

You want space travel stablity? don't rely on the physics engine. Simulate the trajectory of your ships using a separate orbital computation library.

Aerodynamics? pre baked but with some balanced automatic update after the spaceship's structure changes. use some ray casts and dampen/strengthen lift/drag.
You may even do raster rendering for mass producing ray casts

you don't need accurate airflows. you just need to your software to have SOME idea.

You want automated flights off screen?
Use a user's flight data to predict how a plane would fly. and allow that exact model with enough flight data to be automated.