I think this is just another one of those instances where the full thought process of what this can do to the game setting isn't fully thought out. If you can build a factory ship that can go to any asteroid field and use it as raw material to produce any and every component for a warship (including the fissionables to arm the weapons), then once a system has this capability, its trade will mostly end - except perhaps for luxury goods and some newer tech they can't make at home.Then why not remove them from the game? Problem solved. It seems to me that if you are a building a setting based on trade, then some thought should have gone into what that means. As an example, don't make it so that I can use the rules and build a 100% self-sustaining colony for 100 people for about a billion credits. This colony will expand and never drop in TL, because it can make anything that it needs, from mining and building robotic workers up through finished production. If you want a setting based on trade, like Charted Space, then including things that allow this, is a mistake. I personally love them, but it does break the setting.
Edit - How much does a colony of 100 people cost? 1 billion credit.
How much does a colony of 25,000 people cost? 1 billion credits and 10 years. lol
One has to be careful about designing such industrial system as it can radically affect your game setting in more ways that are often predicted.