I don't agree that current Federal laws only apply to FFL's, as evidenced by things that are federal felonies for you - as an individual - to do at home. Suppressors, auto-sears, etc.
I suppose that the particular situation of homemade firearms hasn't been tested in a supreme court case, but I don't see how it's any different than the established case law where individuals are prohibited from doing things, privately, for themselves, by themselves under the authority of the interstate commerce clause.
Just look at the ways the laws currently are, they are all based around the Fed government not having the power to place laws on firearms that are not part of interstate commerce. The NFA stuff is under an exception for unusually dangerous stuff, not the exact legal term, but close enough. I disagree with it, but that is the current state.
Legal to make your own firearm for your own use including without serial number is currently legal - no interstate commerce.
Intrastate transfers don't have to follow Federal Law, some allow transfer of long guns, some pistols, some none. Up to the state. - no interstate commerce.
There are other examples, the reason these are setup the way they are is that the Federal government recognized at the time they could not legally control this stuff. Of course SCOTUS will continue to screw us most likely once it does get tested by them, but as of now, it isn't legal for Federal government to control this stuff.