There are several levels of regulations and guidance that constitute and carry the force of law.
Statute - this is the law as written.
Regulations - The statute is passed to the cognizant executive branch agency to develop regulations. These regulations further interpret and describe what is in statute, but must be consistent with the intent of congress in passing the statute ( and some times agencies get it wrong - sometimes intentionally, other times just through incompetence and a lack of understanding of the nuances and/or practical realities of the issues. Any substantive changes in regulations are supposed to be published for public comment before they are adopted.
Regulatory Guidance - these are formal documents that provide additional guidance or definition, and they are often also issued for public comment if they are substantive in nature.
Sub-Regulatory Guidance - This consists of specific guidance on specific issues - such as ATF response letters to questions. They apply only to the specific issue at hand.
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The level of clearance on sub regulatory guidance is not as thorough and it does not go out for public comment so some of the mistakes made are spectacular. The whole Sig brace issue is a prime example. Shouldering a Sig brace equipped pistol was determined to be legal based on a collection of very narrow legal interpretations, made by attorneys, largely in the absence of common sense. The end result was a huge number of letters from people asking "really?" - apparently because they were too stupid to just see it for what it was - a very fortunate error in there favor. However, since they effectively made the error so obvious and egregious, ATF had to issue revised guidance.
ATF could have simply said "On further consideration and in light of the magnitude of responses suggesting this might be a problem, we've determined that our previous guidance was in error. We've further determined that it looks like an SBR, is shouldered like and SBR and functions like an SBR, then it's an SBR and consequently the Sig Brace is a stock that changes an AR-15 pistol into SBR."
However, ATF again resorted to narrow legal distinctions and decided that use of the object defines the object. Thus they determined that when an AR-15 with a Sig brace is shouldered it is no longer being used as designed, made or intended, and becomes an unregistered SBR. Sig used the example that using a can of corn as a hammer, must therefore make a can of corn a hammer, when they pointed out the absurdity of the ATF argument.
Another more alarming example of where this reasoning runs off the rails is in the ATF's definition of pistol:
"The term “Pistol” means a weapon originally designed, made, and intended to fire a projectile (bullet) from one or more barrels when held in one hand, and having:
•a chamber(s) as an integral part(s) of, or permanently aligned with, the bore(s);
•and a short stock designed to be gripped by one hand at an angle to and extending below the line of the bore(s).
So if we apply the ATF argument that "use can re-define the weapon", and I shoot my 1911 (one of the weapons ATF uses on their website to define "pistol") with two hands, I'm now using it other than it was designed, made and intended - per the ATF pistol definition.
The moral here is that if the ATF can screw up sub regulatory guidance that is subject to some level of internal clearance, then an ATF field agent can most certainly say something in error - and unlike a written letter, that spoken word is of zero use in a legal defense, particularly when it becomes hearsay when repeated by the person who supposedly heard it from the ATF agent.
The opinion of an ATF agent is just that. It's an opinion, and does not have the force of law. It's not smart to ignore an ATF agents opinion, particularly when he or she is telling you something is illegal, but more importantly, you don't want to take that opinion as permission to do something that conflicts with the documents above that do in fact have the force of law. The "but the ATF agent said..." defense isn't a good one in criminal court, as all the prosecution has to demonstrate is that the agent was wrong.
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One other thing to consider is that some laws are not actively enforced as primary offenses. For example, there have not been many (if any) cases of individuals being prosecuted for shouldering a wrist brace or cheek rest equipped AR-15 pistol. That's in part because:
1) the hole shit show described above and ATF's seriously flawed reasoning.
2) the distinction between using a saddle as a cheek rest and moving back some fraction of an inch so that it contacts the shoulder is pretty small, difficult to definitively observe from most angles, and thus is difficult to enforce and successfully prosecute (although an unsuccessful prosecution will still cost you at least 5 figures in legal bills; and
3) It's also a victimless crime, so not too many people are demanding it be rigidly enforced. If AR-15 pistols with saddles, braces, etc, start showing up at crime scenes in substantial numbers, or are just perceived by the public or politicians as being used in crimes, then that will change.
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Where a weapons violation of any type will get used in a prosecution is to increase the potential prison sentence, in order to get the accused to either plea bargain on the primary crime that was committed, and/or roll over and inform on someone else. If you're looking at 10 years in federal prison for a weapons violation, accepting a plea bargain for 5 years on the armed robbery starts looking like a good deal.