The way all factories work in Victoria 2, regardless of economic policy, is simple: profits from the factory are divided between capitalists, clerks, and craftsmen (each class gets a particular percentage, split among all of its members at that factory). These are the wages that the government taxes. No capitalist pops "own" any factories, so switching economic policy doesn't change matters for existing factories. All it changes is who can build and upgrade factories, and whether or not factories may be subsidized.