Actually, it's exactly the first freedom the one missing from physical objects. You are free to analyze Coke with a microscope, but you won't get the recipe. You are free to 3D-scan a fork and analyze its alloy, but you won't be given the original CAD project and the production plans for the material.
I'm not sure if you were implying that the 4F are replicating what happens with physical objects; I would disagree with this. The 4F expect from software much more than we expect from any other good or service we buy/rent/consume.
Ah, but there are multiple levels: You can take chair apart, or split your pants along the seams -- and if you can find a material with comparable strength, or a fabric you like -- you are free to make as many "copies" as you want.
You are free to attach a metal head to a shaft and call it a hammer, and look at other hammers for inspiration, if your hammer doesn't work quite right.
You are of course right that it only goes so far -- and this is perhaps most scary in the field of bioengineering -- with the possibility of a) sterile produce (you wouldn't be able to plant a potato any more), and b) patented/"copyrighted" gene sequences -- making it illegal to plant certain "proprietary" produce without a license grant.
I do agree that the analogy is flawed -- is the shape of a fork more like the api or the source code? I suppose the main difference is that many useful physical things are trivial conceptually (once you've had/seen the idea).
I'm not sure if you were implying that the 4F are replicating what happens with physical objects; I would disagree with this. The 4F expect from software much more than we expect from any other good or service we buy/rent/consume.