Surrender to Toc...
I looked at the editor for the first time. I'm working on an insanely powerful ship to upload to the Steam Workshop that will demonstrate some of the most obvious issues with the current editor. In the end, you are going to have to accept that there will be two groups of ships. The “stock” ships, and the ships people make in the editor. They don't really mix. “Interesting ships” are lacking in some areas and powerful in others, intentionally designed to be interesting. This is the opposite of the ships players will make in the editor where, in modern terms, they will “chase the meta”.
There is absolutely nothing that can be done to force players to make the types of ships that you will want the stock ships too be. If you want to have cool working “interesting ships” like the original Star Control game had, the fact that many of them are actually really bad in one way or another prevents an editor from creating ships that are balanced with them. Players will create ships that have no major flaws, but major flaws are what makes ships more interesting. The points can only account for so much.
So you should probably be thinking of the editor ships as an entirely seperate “universe” than the stock ships that Stardock had designs for the game. If you try to make the editor create ships that are balanced with your originals you will never succeed in that. We already had exactly what you are trying to do with this editor in SFB. S8.0 Ship Modifications. It worked exactly as you are trying to make this editor work. Don't go looking for S8.0 in SFB, all you'll find there now is “Patrol Scenario Rules”. It can't be made to work the way everyone wants it to work. But it can be made to allow players to create a “higher class” of ships than your stock ships.