Research goes across your empire, it's cumulative. If you have four colonies with 1 lab each, you've got 4 labs total cranking out research.
But if you have 4 colonies with 1 factory each it does NOT mean that when one of those colonies builds say, a ship, that you get 4 factories worth of output. A factory, or other manufacturing resource, only increases the build speed of something being built ON THAT COLONY.
So....if you're not building anything on a colony (a ship, or a planetary improvement, etc) any factories on that colony are doing exactly nothing.
If this is true I can see why people specialize planets for manufacturing.
-MB