If you use a performance computer to calculate takeoff performance, it is VERY likely V1 will be increased significantly on the longer runway, and the stop margin will not increase significantly.
In cases such as you describe, I often run several calculations, with and without derates and ATM reductions. I look for a good balance between thrust required, V1, and stop margin.
Also, I will ask for the longer runway when near the performance limits on the short runway.