Let’s talk terminology for a minute.
Proteins are made from long chains of amino acids that may have been modified during protein formation. There are only 20 normal amino acids in most proteins. At an atomic level, lots of carbon atoms, oxygen, nitrogen, and hydrogen being the most common.
To say that something is ‘molecularly identical’ means each of these amino acids appears in the same position in the larger protein structure. Companies are now synthesizing whey protein from cow milk. It is the same protein.
Your argument is that we could take all of the ingredients of spaghetti pasta and sauce, drop it in a blender, and make spaghetti goo that was ‘molecularly identical’ to a dish of spaghetti pasta with sauce. Neither spaghetti pasta nor the sauce is a molecule. There are many different kinds of molecules from various sources. Carbs, proteins, fats, water, on and on. Even further, the blender most likely breaks some molecules and forms new ones. No one would use the terminology ‘molecularly identical’ between two such substances. I don’t even think you could make the claim that a plate of spaghetti and sauce that was dumped into a blender was molecularly identical to the substance before blending.
Like KBLB, Spiber is using ambiguous language. They have a large database of silk proteins. They are making brewed proteins, but these are not necessarily golden orb dragline proteins. Many spiders produce several kinds of proteins. They may very well be working with a spider silk none of us has ever heard of. They may also be incorrectly using the term ‘molecularly identical’ to suggest many protein sequences are the same, even though the total structure may be different, where there are fewer repetitions of sequences, for example.
Having said that, I think my claim that they are working with recombinant spider silk proteins, just as KBLB is, can be justified.