It's important to distinguish between the security clearance required of an organization or staff and a capability required of an organization. It's not necessary for an organization to have the capability when the contract is awarded. However, the organization will need to have the capability when it's required as the contract is being carried out. So it's normal for a contract to be awarded without a capability having been verified through the contract security program.
In the case of GC Strategies, the company didn't need that capability to carry out the contract. The contract was therefore amended to remove that requirement.