How do I uninvert the mouse? There has to be a way. Why would they make games with mouse settings you can't change?

Well, yes and no; ctmouse v2.1b4 can invert the mouse axis everywhere. This would be viable if you were willing to use the keyboard controls to navigate trading menus and so forth (mostly Tab). Another option would be to use a controller for space flight and invert that using the DOSBox Mapper.

That's the best you can do since the early games in the series didn't support axis inversion.

Well, inversion was standard for flight sims back in the day. There was no need to un-invert it. It was supposed to work like in a real plane: You push the joystick away from you and the plane goes down.

In other words, play it with a joystick?

That would be advisable, yes.