Because the $200 tax is required by law, and I haven't seen any statute, or provision within, that allows ATF discretion in collecting it except as provided by 27 CFR § 479.69 & § 479.70, which doesn't include firearms made for personal use by a private citizen.
Perhaps one of our resident attorneys can weigh in on the matter and provide clarification, but to this lay person, the misnomered "amnesty" registration is just riddled with legally problematic things that will take years to sort out in the courts, if ever, and at great expense & hardship to the unlucky ones who are ensnared.