It is the language about how the use of an item can be interpreted as a 'redesign' that is concerning. It may well be possible that an ATF lawyer makes the acting director of the technology branch rescind that letter tomorrow as establishing that precedent would have undesireable implications beyond the ATF. But until they do, it is a sign of differing opinions within the agency on the legality of the device when used in a way that diverges from the manufacturers directions.
This all conjecture for now - we don't even know what the sample was, do we?