[Fyron]

It works by ability. You get the effect of the best of each of the following abilities that affects a planet, regardless of what facility they are on:

Resource Gen Modifier Planet - Minerals
Resource Gen Modifier Planet - Organics
Resource Gen Modifier Planet - Radioactives
Resource Gen Modifier System - Minerals
Resource Gen Modifier System - Organics
Resource Gen Modifier System - Radioactives

Resource Gen Modifier Planet - Minerals and Resource Gen Modifier System - Minerals will stack with each other. But, two facilities that each have Resource Gen Modifier Planet - Minerals will not stack with each other.

Robotoids have 3 of the abilities, either planet or system. You can have a Robotoid Factory stack with a System Mineral Scanner, because one uses planet abilities, the other a system ability. But, a Robotoid Factory and a Mineral Scanner (both of the planet variety) will NOT stack their bonuses to minerals production, only the best value will be used.