Regardless of the weaknesses of the procedures or the competence or lack thereof of the agency, the manufacturers did what they could under the circumstances to ensure the legality of their actions.
I agree with the rest of your post. A well-informed court guided only by constitutional principles would find the NFA to be unconstitutional, and could do so without overturning the original Supreme Court ruling upholding it. The current standard issue military rifle is selective fire and has a barrel length less than 16", which was not the case at that time.
I agree that sound suppressors can effectively be pursued by demonstrating that they are not actual silencers, and do not even necessarily negate the need for hearing protection. They do, however, clearly mitigate hearing loss.
I also agree that shoulder stocks on short barrel weapons can also be effectively pursued. Very few mass shootings have occurred with such weapons, and enhancing the accuracy of a lawfully used weapon benefits everyone - lawful defenders, bystanders, etc.
Yes, full auto weapons are a bridge too far. From a purely constitutional standpoint, they should be allowed. However, the judges will not operate in a vacuum, and they are going to be thinking about being blamed for enabling the next Las Vegas event. As lawful defender who are accountable for each and every projectile we launch and who must pay for our own ammo, we have no real world use for full auto. If society totally collapses, we will need to preserve our ammo and use it effectively.
We appear to be several months away from some favorable Second Amendment Supreme Court rulings, perhaps setting a standard of review. Those rulings will likely include some dicta that could form the basis for insulating at least some parts of the NFA - if not the entire NFA - from attack.