I know, if I need to reduce empty space, I select each part and I change the position manualy. If you do this and you want to import an other part, don’t forget to uncheck the auto position function or you can start al over again. Been there, done that.
also a nice feature in simplify is that you can use multiple factory processes in one single part. you can set a z-dimension where to start the process and where to stop and continue with another.