[Fyron]

Ok... how about this:

You get the best bonus from all "planet-affecting" facilities on the planet for each of the three resources.

You get the best bonus from all "system-affecting" facilities in the system for each of the three resources.

These two bonuses add together.

Example:

Build System Mineral Scanner II (+20% min), System Robotoid Factory III (+30% to each resource), planet Eco-Farms III (or whatever it is called: +30% orgs), planet Robotoid Factory II (+20% to all resources).

So, for all planetary bonuses, you have:
org +30% EF
min +20% RF
org +20% RF
rad +20% RF

So, the best of these is:
min +20%
org +30%
rad +20%

Then, for the system facilities:
min +20% SMS
min +30% SRF
org +30% SRF
rad +30% SRF

So, the best of these is:
min +30%
org +30%
rad +30%

Now, add the best planet and system bonus for each resource:
min +50%
org +60%
rad +50%

These are the final bonuses you get.