For sure the dimension is M3. I had a dozen of duck eagle/viper in various versions and various colors. I bought more than a hundred of extra screws according to this dimension and they fit well. Since I found the bolt holes of M3 5mm screws coming along the kits are not very well fit to my screw driver, I usually use these extra screws for assembling.
It's common for a kit to have the same diameter on all screw holes for one part of the construction. If you design a kit or manufacture it, you will realize it's unnecessary complicated, and silly to use different diameters for screw holes in this situation. So it's impractical to have both M3 and M2.5 in this viper/eagle case.