When we design airplanes, we do it to safely operate at various runway lengths. And we do that by providing those various speeds that you find in your AFM/CAFM/Performance software.
V1 is your safety speed defined based in a multiple factors. So it doesn't matter if you have more or less rwy length left. Respecting the calculated V1, it doesn't matter what engine rate/rwy length/whicheverfactoryoudesiretojustifyyournonsense you chose.
So, as it was stated before, both runways are safe. If your AFM/CAFM allows you to TO from a particular rwy, than you should go with the company's policy of cost efficiency.
Repeating what @Piltdown Man said "If the numbers say you are good to go, then you can go."