It confirms that the policy is that students who lose their ecclesiastical endorsement due to disaffiliation are expelled from the university, but that there is an exception process students may seek. BYU's spokesperson says that such exceptions are rare, but the article doesn't give any color as to how frequently they are granted.
"BYU’s Honor Code explicitly states the principles students are expected to follow," Jenkins said. "For members of The Church of Jesus Christ of Latter-day Saints this includes following the values and standards of their religion. Because of covenants and commitments members of the LDS Church have made, they can no longer remain in good Honor Code standing if they go through the formal process of removing their names from LDS Church records. The Honor Code states that students are required to be in good Honor Code standing to be admitted to, continue enrollment at and graduate from BYU."
"Excommunication, disfellowshipment or disaffiliation from The Church of Jesus Christ of Latter-day Saints automatically results in the withdrawal of the student's ecclesiastical endorsement and the loss of good Honor Code standing," the section states. "Disaffiliation is defined for purposes of this policy as removal of an individual's name from the official records of the church."
The policy is explained in the “Withdrawn or Denied Ecclesiastical Endorsement” section of the honor code.
Exemptions are rare, Jenkins said. In such cases, the student pays the tuition of a non-LDS student, which is double that of an LDS student. Church tithing supports BYU, so all Mormons who tithe support the university. Tuition this year is $5,300 for LDS undergraduates and $10,600 for non-LDS students.