1. Yes you can mismatch them i.e you can assign them to any station regardless of their qualifications.
Sorry I meant historically, ie were officers assigned specific positions or did they rotate? Basically is it realistic to have an officer that is a machinist but also a weapons expert?
2. Yes we(I) always use Helmsman in the control room. The reason see no.1
Got the impression from seaching the forum that helmsman didn't have any effect?
3. I have yet to have a crew that good, especially after one patrol.
Actually I played with importing some officers

A 500 experience officer with torpedo qual would only need 2 qualified warrant officers to get 100% efficiency, maybe a couple of seaman at most. For the engine room this guy only needed one machinist and two seamen. Seemed wrong that I use just a fraction of the crew. (note I'm going to reload it and not use this guy, feels wrong to just import an experienced officer, although I'll probally choose officers qualified for torpedo and machinist, seems wrong that you don't start with guys qualified in these).