two different issues. ref. security clearance, the most basic one is just like the no criminal record from police. If you apply for the security guard in airport, cleaner in an office building or a job in government. Of course, there are different degree of requirements on the security clearance, eg if you work for the department of defense, even the citizens needs higher degree of clearance, or may not pass the security clearance.
Citizenship approval do not need the security clearance.