Just change the Sizemod attribute on the desired part in GC2Types.xml (sizemod is the % of the hull's size that is added to the base size to get the final size). Setting it to 0 makes the part be just the base size. Negative sizemods are also possible, which would allow you to make part that are impossible to put on smaller ships but take up little space on bigger ships.

I imagine that this has been answered elsewhere as well. I understand why engines and defenses and life support scale with ship size, but it makes no sense to me that other components such as weapons should scale. Is a 5 mw laser on a battleship really bigger than it would be on a gunboat?

I still question whether or not the upward stacking and scaling of all the numbers in GC is a good thing, but as long as its working, I guess it's okay.

One thing that I think would be a good mod (or option) would be to restrict ships to having only a single engine, which would curb the speed 50+ invasion transport fleets late in the game.

All in all, I'm fairly pleased with the DA changes, but I've only played with it for a few hours. The only combat I had was an invasion by a certain faction that gave me quite a bit of grief, but was a good test of the combat system. Under the old system, my defensive squadron of tiny interceptors would have barely been able to scratch the enemy "frigates", but under the new system, the fight came down to the final hit point (I lost, but it was very interesting).