• Whilst you can't set one-per category, I did notice that Hypergate Components (for example) preclude particular choices of other components. You could use this method to achieve the affect, by adding every other component of that category as a preclusion. Annoying... but doable.
• Admiral abilities can certainly be done... probably Privateer. I've in fact done something similar with commander components/etc. in GRM. 
• If your civilian engine is much larger, but cheaper... I'm not certain it really is necessary to restrict it to cargo hulls. If I want to spam inferior ships... is that so bad? But it is an interesting idea. I've had some ideas for tweaking hulls and this would potentially help. I'll look into it.

In answers to your remarks:

1) too much bother about this 'one per category'. My modding and gaming time is quite limited, so if I do another  mod I'll instead take another approach. If I create a line of components, then I'll assume the player will end up using one of each, like the stellar accelerators. So the solution is to have each one doing more or less as the previous one, with only a very small benefit (like reduced mass). This way you can pile them up as you want, it is expected. The error would be to have say SA I giving +1 move, SA II, +2 moves, SA III +3 moves. You can bet a player will have ships with +6 moves (that I call 'Fleet Tugs' and use in vast number to move combat ships around    ). So instead, each will give +1 move. And then you can pile them up, as expected, to end up with your ships with +3 moves if you use them all.

2) The interest of restricting a component to a hull is also to make sure the AI is not botched by it. I don't want it to use civilian engines on combat ships i.e. Also it gives flavor. I might want to restrict a weapon to tiny hull... And definitively don't want it to be used in vast quantities on a large hull.

3) I saw something that looked like the privateer option in a file, but that's not too clear. It seems to make the ship a pirate?