When a logistic group gets set for a spaceship it sets the pickup to be the default location. I.E. Stack Inserters are requested from Gleba. There's no way to change this though, because if you update it, the update gets immediately overwritten by the logistic group combinator. Not sure if there's anything that can be done, but if there was it would make setting up my on demand spaceship cargo hauler a lot simpler.
