Honestly, I would just have two versions of each faction: a "human" version and an "AI" version...with separate player files, these factions could have completely different tech trees and building options for structures and ships...
At each game start, you'd want to make sure all the slots for AIs were filled with AI versions, of course...so one limitation is that you couldn't really use random...
Another possibility is to add technologies that appear "offscreen" by having the tech icon in the tech tree appear in a location you cannot see via the UI...if you can't see the icon, you can't click on it, and if you can't click on it, then you can't research it...doesn't affect the AI because the AI doesn't "use" the UI....
This allows you to add researchable abilities or prototype technologies...if you make the tech have no lab requirement or cost, you start with it for free, so you can even grant the AI bonuses (or penalties) from the very beginning...this method is good for adding additional things to the AI's arsenal...
It seems though that you are looking to give the AI capital ships that don't require fleet supply...I think you would need to have a duplicate player file that gives the player a different roster of capital ships (the duplicate caps that are the same in every way but don't require fleet supply)...
Also, don't forget that each capital ship has an unused ability slot....this "slot" is graphically covered up by the ability management button, but you can still put abilities there and have no stability issues...one problem is that if this 5th ability is an active ability, a human player cannot click on the ability button (because the ability management button is covering it), so usually this 5th ability needs to be passive...however, if you only added 5th abilities to the AI versions of capital ships, then it wouldn't matter, as the AI would still be able to use the ability...
If you don't want the 5th ability to use ability points, you'd need to change the levelSourceType to either an ability that inherently comes with the ship no matter what, or one that is available after a certain research requirement...