Fifty years was a long period of time. Atlas' current lifetime was not even that long. However, in terms of the current situation, it was no more than a blip.
In fifty years, how much could the Neurics develop? With their exponential growth rate, it may have seemed like they could go out and conquer the continent immediately, but it wasn't that simple.
The ones who conquered the continent would not be the Neurics, but instead, the Igni Neurics that they evolved into. In other words, the current generation was not going to be the same as the one who saw the light of day for the first time.
They were only creating the stairs that led to the surface.