I’m absolutely not certain of this but I would think it may be an issue. If you choose to apply both the GCB and NCP to the car, you are choosing to pay a little over £1000 which would absolutely be over the 50% of grant limit. As the NCP can be paid direct to you after getting the car and the GCB is absolutely paid direct to you after getting the new car then they may both count as your contribution.
At the same time, if they consider the NCP to be a reduction in the AP, then the actual AP is then £1349 which after the £999 grant leaves less than 50% of the grant to cover the difference.
I typed this with one idea in my head then talked myself into the second (completely opposite) possibility so now I’m as confused as you seem to be.
All I can suggest is don’t ask here as I doubt anyone here will know 100% unless they have been in the exact same situation – only option I can think of is ask someone who WILL know, either Motability or the grants team.
It basically all comes down to if they consider the NCP to be your contribution (which technically I think it is as you CAN use it but don’t have to) or if they consider it to be a Motability reduction in the AP.
"Man is born in freedom, but he soon becomes a slave, in cages of convention, from the cradle, to the grave."