Presumably there must be a lot of computer assistance?
For example, Xpedition's sketch routing feature: https://www.youtube.com/watch?v=fIi13gI9xEA
Routing 4094 signals sounds daunting, but it is a bit less daunting when you realize that a good fraction of them are power/ground (and route directly to planes), and the rest of them are mostly logically organized into buses/groups that can be routed together.
Seems like it's almost boring these days since everything's encapsulated in a layer of abstraction. A lot of the more complicated wiring is in breaking out PCI-e channels into things like ethernet, audio, and other miscellaneous ports that involve good chunks of analog circuitry.