I think a lot of it depends on the specific application. In the case of a PC motherboard, there is already a lot of IP with regards to design rules, constraints, connector / component libraries, modules (CPU PSU, PCI-E array, additional USB + SATA etc). Intel and AMD also have their own reference design, which manufacturers adhere pretty closely to. In other words, it is just an evolution of existing designs.
In my case, I do a lot of RF and "mixed signal" work. Inherently, these lend themselves to a modular design. So, in the early stages, you can hack together your own module, or buy an off the shelf "whatever"; for example a DDS oscillator, mixer module, 10.7MHz IF strip etc. Just how far you want to go with prototyping is down to the engineer's judgement of their own ability and experience. It also depends how quickly other people need real hardware to start developing software with, or for hooking up to other hardware.