Is the Warrant and Ship Origin path supposed to operate like the character origin path? In that depending on what you pick, you can choose the option either directly below or one space removed? If this is the case, it seems odd that Reward is a choice for Fallen from Grace and Exile is a choice for Rising Star. I would have reversed their position.
Into the Storm- Ship Origin Path
You will notice that the first line gives lots of pf and sp on one side, while the second line gives lots of pf and sp on the other. That is the reason why you are supposed to only pick from the next line below or adjacent. It doesn't matter much after the first two rows as all subsequent rows give the same summed pf and sp.
If you want to use a bit more freedom, than the easiest way is to the pf/sp from the first rwo completely and add it to the corresponding option on the second row, and allow any ship to choose one archaeotech or xenotech component at creation regardless of warrant choices. This makes the warrant choices mechanically balanced, though SP is still strictly superior to PF unless you have a child of the dynasty because unspent sp becomes pf anyway but this is a fairly easy issue to fix if it even is an issue for your group.