Don't have access to a MEL, not sure if this is correct but my experience with Airbus manuals and their logic would indicate:
You don't use the failure factor because you have not had an in-flight failure. You have despatched with SEC 3 INOP which is a different situation, and is therefore treated differently.
And also as an aside:
The 5% MEL correction is at the planning stage, and I reckon it should be on RLD which is approximately 1.65 times ALD.