In this case I would advise to create a user role 'Administrator', as this is exactly what it is intended for. If you go route B it will add extra maintenance work for that association.
Scenario A: When you set the company for the administrators, they will automatically get the correct permissions.
Scenario B: When you set the company for the administrators, you will also have to set the association to the employee. Also when an employee changes company for instance, you will need to update it.
A is the way to go, as it's easier to maintain