Full description of build at source.
 
So what’s the headcanon story behind it?
 
Instead of being made at the weather factory, the colorant for rainbows is obtained at Rainbow Falls. The problem is the spectra is mixed in with water at about a 20-80% ratio, so it has to be separated, which is where the factory (or refinery) comes in. The mixture is pumped into a tank where it’s heated up by a coal fired furnace/boiler, then it’s pumped into the fractionating tower where, with the heat and a little magic, the colors are separated from each other and the water, with purple being the heaviest, and red the lightest color From there the colors flow into the holding tanks.  
Meanwhile the now purified water is sent into it’s own tank, while any steam generated by the process goes into a condenser and is pumped into the tank also. If the tank get’s full, a couple of valves are turned and the water flows back into the stream through a pipe that comes out on the other side of the low water dam.  
Though they’re present in the stream, intermediate colors like cyan and indigo are too close to their parent colors in makeup, so they’re separated back into them in the tower. If these or any other colors are needed it’s custom mixed at the weather factory.  
When spectra is needed, it is pumped out of the storage tanks and into the tank cars for shipment to a point under Cloudsdale. From there pegasi use small tanks to offload it and take it to the factory. The spectra is also shipped out to other places to be used in dyes, paints, crayons, and with more refinement; food coloring (ask _Pinkie what happens when you eat it raw). Likewise the purified water is good for cloud and snow making, so it’s also shipped to the point under Cloudsdale where the pegasi lift it up to the factory with the tornado method. It’s also shipped to a bottling plant and sold as Rainbow Falls Spring Water.
 
 
Hey, it’s nicer sounding than the other way of getting rainbow coloring.