From the article:
But what the IRS ultimately objected to was the way the CDD's governing board was set up.
...
"We believe that an entity that is organized and operated in a manner intended to perpetuate private control, and to avoid indefinitely responsibility to a public electorate, cannot be a political subdivision of a state," the IRS wrote in its ruling.
The IRS isn't merely questioning the tax-exempt status of some bonds but the form of "government" created to issue those bonds.
Obviously, the IRS can pursue the matter through the Courts if WDW decides to fight. This includes Federal Courts that are not in Disney's back pocket, the way Florida's government is.