A while back I hired an EE straight out of college. He asked me something like, "how do you prove out your designs? Do you breadboard them? Wire-wrap? How?"
My answer was, "Well, we build a PCB and if it works we go into production and ship it!"
Many circuits simple cannot be prototyped without making a custom PCB. Anything high-speed, low-noise, high switching currents, etc. are difficult or impossible to make any other way. Sometimes the logistics alone get in the way. You cannot, without a custom PCB or some crazy adapter/socket, prototype with a 1000+ ball BGA. Even if you could, you wouldn't want to. The odds of making 1000+ connections without error is very low. Doing it twice is almost impossible.
Making custom PCB's for prototypes seems expensive, but it isn't. Not compared with paying someone to make and debug several prototypes using breadboards or wire-wrap and even then ending up with something that is of questionable reliability.
So professional EE's usually go straight to designing a PCB and then doing everything they can to make sure that PCB works the first time. It almost never works the first time, but the closer it is to working the better it is. Then the board is modified (a.k.a. re-spun) and built again. With any luck a PCB goes through 2 or 3 respins before going into commercial production.
I recently did a custom PCB that used an Intel Atom PCB and all the usual PC type things. My approach was no different with this PCB. I designed it, tried very hard to get it to work the first time, and built it. The Rev 1 PCB's mostly worked, but has some minor issues. The Rev 2 board worked perfectly.