[Keroko]

Another conclusion is that Mikoto's Railgun doesn't work like normal Railguns.

The general consensus seems to be that Touma can block things as long as they are affected by a supernatural phenomenon, right? In that case, his ability to block Mikoto's railgun would mean that Mikoto's railgun doesn't work like a normal railgun (accelerate with magnetic fields then fire) but rather the entire process of accelerating, firing and hitting are constantly guided by her powers. The visuals of all sources do support this, as we see constant arcs of electricity along the entire course of the projectile.

This way it makes sense for him to be able to block it, just as he did her iron sand sword, Sheryl's golem and Misha's blast of water, all three of these were manipulated forces and yet by merely canceling the powers manipulating them Touma was able to reduce their momentum to zero.