No, the S&W origin path system doesn't have to be balanced with itself. And balance main issue is combat, nobody cares if your explorator has a unfair advantage in tech use or your senechal knows all forbidden lores.
Balance is needed to give fairness to all players in a game. The S&W origin path affects all players equally as they are part of the same crew on the same ship (unless you have several groups interacting with each other in the same campaign). Thus balance is not required.
If you feel that your players are screwed because they have 30 SP instead of 40, it is your perception and has nothing to do with balance. As a GM, you have to adjust the opposition accordingly.
Your expectations toward FFG and this system are conceptually irrealistic.
If you dislike this system so much, my suggestion would be to use it for fluff only (ignore the mechanics) and use the rulebook version to determine profit and ship points. Or you can create a point based system and give a value in SP to archeo and xeno components.