Manually prerouting dense circuit boards has a strong return on investment. It maximizes routing channels, keeps things organized, and gives the autorouter breathing room for escaping routes.
By placing any high pin count devices and their fanout vias on a sensible grid, the autorouter can achieve the best practical completion rate and the number of layers needed to successfully autoroute the board can be minimized.
The time taken to preroute pays off in noise immunity as well. Planning ahead allows the smaller value bypass capacitors to be placed immediately at the power supply vias of the FPGA, maximizing their decoupling utilty. A skilled PCB designer can find a surprisingly large number of high-value locations for bypass capacitors distributed within the via array of the BGA. As the usefulness of bypass capacitors decreases rapidly with increasing distance from the power supply pins, these close locations are worth pursuing.
A more subtle, but nonetheless important effect of prerouting, is that subsequent product revisions are done quicker easier. The designer can simply implement the required ECO into the layout database that preceded the autoroute step, "top off" the preroutes, and re-autoroute.