I think I can help with a couple of these items...
3) The game does not distinguish between cargo types in that way... a component that has the Cargo ability can store any kind of unit or population, up to its maximum capacity. The difference comes into play when deploying the units (i.e. a mine-laying component can hold any cargo, but can only launch mines). In a pinch, I've used out-of-service sat/mine-layers to drop troops and move population..it's all cargo to the game.
4) I personally don't trust the ministers to do things the way that I feel they should be done (then again, i'm the kind of ruler that wants to know exactly what all of my colonies are producing, and to direct the course of all of my fleets
). Occasionally I've tinkered with an AI's designs (to get a feel of how/why the designs were made), and I've noticed that the AI will overwrite whatever changes I might have made to their designs..even if mine might have been more efficient. From what I can tell (and I might be mistaken, there are quite a few people here who are much more knowledgeable about the AI's than I am), you'll either have to design all of your own ships or have to deal with whatever your minister cooks up..it'll tend to use its designs over what you might have made.
edit: pleh.. I took to long to write up my reply, and AT beat me to it
