The United States is concerned that the Taliban will use Afghanistan to provide sanctuary to groups or individuals that will target the U.S. Government.
“Ungoverned spaces, let alone a known terrorist organization like the Taliban dominating a nation, is altogether an ideal breeding ground for disparate terrorist groups that threaten the United States to find save haven and shelter,” said Marc Polymeropoulos, a former C.I.A. officer who spent much of his career working on counterterrorism operations, including in Afghanistan. (As quoted in this NYT article.)
In an effort to prevent the Taliban from using Afghanistan as a safe haven for terrorists, the U.S. has asked that the Taliban promise to refrain from giving threatening individuals the necessary travel documentation to enter and live in Afghanistan. The visas, passports, and permits mentioned in the agreement will presumably be valid in Afghanistan, but the United States does not have to accept them if someone tries to use these documents to get into the U.S.
It is important to remember that the Taliban acted as the government of Afghanistan between 1996-2001. Its government was known as the Islamic Emirate of Afghanistan. Any government (even those run by militant organizations) needs to have some system of managing its citizens and documenting who travels in and out of its territory. For example, when the the Islamic State controlled territory in Iraq and Syria, it issued birth certificates, maintained DMV offices, and kept tax records. If the Taliban resumes control of Afghanistan, it will likely need to take on governmental functions, such as issuing passports.
