1. As harpo mentioned, you cannot make a mod to do that. If you want all max level capitalships to be the same (all the abilities unlocked), you have to reduce the ability counts so that they add up to 10, such as the 3/3/3/1 distribution Sins capitalships had before Rebellion. The extra level they added so you'd get a 4/4/4/2 spread was to encourage specialization of capitalships my making it so they COULDN'T max out all the abilities.

So just reduce the max level counts back to 3/3/3/1, and if you want them to be just as good as they were before buff the values to that the level 3 ability is just as good as the old level 4.

2. Did you see if this happens several times? Artifacts that you spawn with Galaxy Forge can be replaced by the randomly spawning ones. So if a phase jump accelerator happened to spawn at the planet you already had the Kinetic Intensifier at. To make sure this doesn't happen, you'd have to set the artifact spawn chance to zero, since a planet can only have one artifact.

Might you be using a template that places phase jump accelerator? If that's the one that gives wormhole travel, it is sometimes force spawned on homeworlds with a template on maps that are wormhole heavy, like Ancient Gifts.

Other than that, if you're not using a mod I have no idea why that might happen. I double checked the galaxy forge files and it seems to be pointing to the correct artifact.