At work we're designing highly complex metrology gear. Each specific section has its dedicated developer, for example all the analog stuff is done by one person, basically from signal input to the output of the ADCs. Then another one designs his signal processing part, basically with "open inputs" expecting the mating signals from the analog person. his processed digital stuff combines also the user interface (another person), display (also), and external digital interface stuff (this he actually does by himself). Another one takes care of the power supply and so on.
In the products we design this is relatively easy to do since many of the parts are strictly separeted onto different boards, so only the connectors, their positions and the signals and their connections on the pins need to be discussed, after that everyone can design his own thing. But you can surely use the same approach for single board systems, you just have to carify who gets which part of the pcb to work with.
(You may notice that I have generalized a bit, but you get the point.)
We route everything by hand btw, no autorouters involved.