If an applicable large employer takes advantage of a safe harbor, does it have to use the same safe harbor for all full-time employees who do not enroll in coverage?

In other words, does a safe harbor apply to the whole group or on an employee-by-employee basis?

No, depending on the circumstances an employer might meet the requirements of one safe harbor for one employee and a different safe harbor for a different employee.

The employer might also use one safe harbor for one class of employees and another safe harbor for another class of employees (for example, W-2 for management employees and rate of pay for hourly employees).