Reread the section of Desktop Manufacturing, Arsenal p.130-131. Part of the problem is that the megacorps realized they made a mistake in inventing those, because they cut too much into their profits, so they are limiting them every way they can think of. And for starters, but only manufacturing (or at least selling) feedstock riddled with stealth RFID,
As for removing the tags, well:
<quote> ...feedstock in the form of a special plastic powder with metal fibers and microchips/tags mixed in ...</quote>
Apparently the feedstock needs to have its own microchips and tags mixed in so the desktop forge can use it (presumably so it can check the progress, align the right fibers, and so forth). So good luck separating those from stealth tags ! And afterwards, well, destroying a stealth tag is not easy, it's extra hard to locate and you have to bring your tag eraser within one centimeter of it, so if you are making a large piece and it is in the center that may not even be possible... And even if the piece isn't too large, you could still 'miss a spot'.
You still have some options, like an EMP pulse or some tailored Detect Stealth Tag + Destroy Stealth Tag spells, but is it even worth it ? Remember, this started as a discussion about making some cheap bootleg guns !