Except there are literally lore reasons that explain exactly why they can do that.
There are multiple types of FSD engines for jumping between systems. the version that are in capital ships are able to make precise and extremely long jumps. But the cost of this, is extreme size and fuel in order to make that jump.
The version of the FSD that is in the pilotable ships are a newer version of FSD that while smaller, retain a sizable jump range, at the cost of jump accuracy, while also allowing for hydrogen to be used as a fuel source rather then other materials.
Thats and established lore thing.
Source: https://www.youtube.com/watch?v=JyKdBTi7B1U
a video by one of the guys that writes for the universe.