There has always been a contingent of people that do sensitive work for the government because they have important expertise but are either "unclearable" or unwilling to go through the formal clearance process. Limited affordances are sometimes made in these cases at the discretion of senior officials with that authority. For the government it is a practical risk/benefit calculus and they still have the ability to do a substantial background check on their own without a formal process.

While it would never be allowed for the average Federal employee it does exist outside of purely political positions.