NCS does not have discretionary powers, these belong solely to the Directorate. The NCS can however determine if you have met all the 'hard' requirements. And if the NCS thinks you do not qualify they can say so and refuse to endorse your application.
In that case you can simply apply directly to UKBA without using the NCS. As we all know, there are criteria for which even the Directorate has no discretion, and to avoid a refusal you will need to be real sure that your deficiencies fall within the discretionary range.
Take note that if you are refused, take care that fixing your absenses will require time and that might kick you into BCI's commencement, and nobody knows how that's going to work yet.