Congress and the president control processes such as passport issuance by passing laws, which are subject to judicial review.  Within the framework of the three-way checks and balances, therefore, the federal government as a whole is responsible for determining the rules for such a process.

The income tax process is also defined by federal laws.  Since the federal government controls both processes, it is free to create interdependencies between those processes.  For example, it can require passport applicants to give their social security numbers if it wants to be able to cancel the passports of those who are delinquent in paying their taxes.