In court, the issue is presence of evidence. Absence of evidence of doubt. The government didn't produce evidence to the contrary, and therefore didn't even probe an element of the crime, let alone prove it. IOW, the alien made the claim, and the government said, "ok."
You asked about the reason, a "why" question. I speculate that the government had been getting away with sentence enhancers for years, using the threat of ID theft, but not taking the time to present evidence and an argument. Laziness, facilitated by compliant courts. A lawyer notice the absence of proof to an element, and lost all the way to SCOTUS.
If you ever get the opportunity to study law, and then see how it is practiced, you'll be amazed at how sloppy and error-ridden the institution is.
Law, as this layman sees it, is, at the conclusion of the matter, all too often a vehicle or a tool used by the unscrupulous to dodge or minimize the consequences of their conscious actions.