For SE6? Available planet tonnage should just be a single pool.

I have been wondering why a planet colony has specific room for facilities and a separate space for cargo. What's up with that?

A planet should have an amount of "available" tonnage for building things. Out of that tonnage, we should have Living Space for our populace and space for facilities. The facilities can and should be different sizes, e.g. a Farm should be bigger than a Research facility. The Space Port should be pretty big and the Ship Yard should be the biggest one.

If we want cargo storage, we should build Cargo facilities. Cargo can still be generic, but should not include Weapons Platforms. I don't know of any military that keeps planetary defenses stored away in warehouses (but then I don't any of these military groups anyway).
The weapons platforms can still be considered cargo for transport to other planets.

I guese that would mean that we need a new facility, Population Living Quarters. With my other post on making population more important to building, running and maintaining things, we won't be able to cheese-out by using the necessary Living Quarters for production facilities.