Two part response:
"It's stupid to have to do that." - yes it is. However, as the author points out, states are broke, so they do everything they can to maximize revenues. (California is horrible at this, they twiddled two of the digits in my social security number and the first I heard about it was a tax lien filed against my house, really sad.) For a long time not filing a tax return effectively deferred your tax liability until you did. They aren't willing to wait that long any more.
"As for the guy in the article, there isn't something quite right." - Of course not, tax stories like this are always more nuanced than the 'victim's point of view. Combined with the common practice of "interpreting" the statutes to mean one thing or another, its what keeps tax attorneys gainfully employed.
Of the latter my favorite is the "home business" or "hobby" interpretation. Your home business of shipping coal to New Castle may be losing money year after year, but the IRS doesn't technically get to call it a hobby, even if there is no evidence to believe it will ever make any money. People abuse that "loop hole" all the time, it is an opinion of whether or not its a "business" and the IRS isn't technically allowed to make judgements along whether it is or isn't. That doesn't stop them from trying to intimidate people though.