1: Go to Interface in the options menu and de-select the box that says "Remove all functional components when upgrading a ship design" (or something like that). That should take care of it.
2: The core designs have a number of weapons and other components that exist only as "jewelry", but don't actually function. While it may look like the core ships are more advanced, they are actually pretty bad against most anything else. Space Militarisation won't really let you build good ships anyway, you'll need to research better weapons.
Also, while this is just my opinion, I consider the AI autodesigner seriously flawed and usually just shut it off (also an option), as you can't set a weapons/defense ratio or focus on engines or other 'noncombat' components.
(off-topic) The last is a particular pet peeve of mine as, if there is one area where the AI opponent fails completely in designing ships, it's ignoring engines. Hence one advantage I will almost always have over the AI, if nothing else, is speed.
Hope all this helps. By the way, there are certain issues with playing the Dread Lords campaign off the Twilight expansion; you may want to play it with the original game instead.
