The base values are the same for all ships (unless they "cheat" by having balance_strength_multiplier). I'm not sure what they are either, but there's a lot of interlocking pieces that determine what they are (such as the "engagement length" setting which I can't remember the right name for, which globally changes the time it takes a cap of 1.0 DPS ships to kill a cap of 1.0 HP ships of the same Mk that they are "good" against.
So if the global engagement length setting is set to 7 seconds, it takes 7 seconds for a full cap of bombers to kill a full cap of missile corvettes IF you take off all the traits that modify their HP and DPS (and assume they are in range 100% of the time, and assume that no DPS is ever wasted).
So instead of modifying values, you're really modifying the ratios. So when I modded the default ships, I went in and tried to figure out how much each trait was "worth" to me, and then assigned the traits to the various ships. (I had a weird balance mod where all fleet ships shared the same defense (evasion), all starships shared the same defense (armor) and all turrets shared the same defense (structure) (oh, and all supercapitals like flagships and the Ark shared the same defense: capital), then balanced under the idea that fighters needed to kill fleet ships, bombers needed to kill turrets and missile corvettes (renamed torpedo corvettes) needed to kill starships (and then the starships became destroyers for killing fleet ships, cruisers for killing other starships, "mobile railguns" for killing capitals, etc. The game became super-tactical, but made the fights take more micro (thankfully not enough I had to pause) to win.)