As Anibal points above/below, generating the SQS and using it for a surface calculation are two separate things, and shouldn't affect each other. You would still take all precautions as usual while performing the DFT calculation.

That being said, there could be scenarios where you may want to restrict/prefer certain atom types amassing at edges or corners of the surface. A friend who studied cutting tools, and materials like diamond or silica used thereof, was very peculiar about atomically uniform edges. As always, it's all system dependent. Let your intuition roll!

As Anibal points in his answer, generating the SQS and using it for a surface calculation are two separate things, and shouldn't affect each other. You would still take all precautions as usual while performing the DFT calculation.

That being said, there could be scenarios where you may want to restrict/prefer certain atom types amassing at edges or corners of the surface. A friend who studied cutting tools, and materials like diamond or silica used thereof, was very peculiar about atomically uniform edges. As always, it's all system dependent. Let your intuition roll!