If I am understanding the system correctly (and we are only getting hints at it now), looting specific crates will reward magazines associated with those crates (i.e. weapon magazines for shotgun messiah crates). If you perk into specific perks (say Gunslinger), you will see more gunslinger magazines when you loot the shotgun crates, but still see other weapon crafting magazines in those crates. You won't be seeing magazines for crafting tools though unless you open a Working Stiffs crate.
The original question that Laz answered was about building POIs. Some POIs are specific to a brand (for example Working Stiffs) which is why when you loot them today, you see a lot of Working Stiff crates in them. Other POIs are more random (for example houses) so you should see more variation. However, deep down it all depends on how the POI designer assigns the types of crates to that POI.
So if you are looking for magazines that would be found in a PassNGas crate (vehicle crafting for example), your odds of finding the PassNGas crate in a Shotgun Messiah store is low, but high if you are looting a Gas station or car dealership. If the POI was setup with a random crate placeholder (for example a house POI), you would just have a random chance of getting the PassNGas crate.