The US never affirmatively recognized Scientology as a legitimate religious organization. Rather, Scientology fought a prolonged, dirty war with the IRS and came out the victor when the IRS decided to settle. Because of anti-tax sentiment that daemonizes the IRS, the IRS doesn't have the stomach for prolonged battles that play out in the media. The public is too credulous when the defendant invariably plays the Samson & Goliath card. (Trump has also successfully used this technique. I once had a law professor who worked on an IRS case against Trump, and he had some interesting stories--not to mention strong opinions--regarding Trump's business practices. Actually, anyone of means caught in the IRS' cross-hairs will use this technique. But you have to be particularly bellicose, as in the Scientology and Trump cases, to flagrantly violate tax laws with the intention of taking the IRS to the mat.)
It's also worth pointing out that, unlike some other countries, the US doesn't really have a formal system for recognizing religious organizations. AFAIU, the closest thing we have is the IRS adjudicating in the first instance Federal tax exemption status. Otherwise, as a general matter, a religion is as a religion does, and it's usually up to agencies, municipalities, and ultimately courts to decide on a dispute-by-dispute basis whether an organization, group, or person is owed the benefit of some particular religious exception in law.
It's also worth pointing out that, unlike some other countries, the US doesn't really have a formal system for recognizing religious organizations. AFAIU, the closest thing we have is the IRS adjudicating in the first instance Federal tax exemption status. Otherwise, as a general matter, a religion is as a religion does, and it's usually up to agencies, municipalities, and ultimately courts to decide on a dispute-by-dispute basis whether an organization, group, or person is owed the benefit of some particular religious exception in law.