Unfortunately, in my experience, it's as haphazard as you describe, moriarty. Sometimes only including new values to the modded ruleset works, and sometimes you need to copy over the whole type, including the stuff you didn't touch.
In a few cases of my own, I had modded:
1) ...the Psi-Amp to use 60% TUs instead of 25 fixed TUs (changing flatRate to false in the process). The result was soldiers somehow never having enough TUs to use the item. SupSuper tested it recently and it seemed to work correctly, so it might've been fixed. I preferred to stick to a flatRate of 40 TUs.
2) ...the power of the Hovertank/Plasma's plasma cannon, and added an auto-shot to the Heavy Laser. In both instances, the bullet sprite disappeared. That was fixed in a very recent build. Oddly enough, I had tweaked the damage of the Hovertank/Launcher's Fusion Bomb, and the projectile never vanished.
3) ...the minimum psiStrength and psiSkill for X-COM soldiers (for less sacking micromanagement and easy screening, respectively). Having left all the other stats untouched, they generated in wild amounts, positive and negative, in the hundreds or thousands. I solved the issue copying over the whole soldier generation block, with all the minimums, maximums and caps, just in case.