Off-the-shelf components make for cheaper computer hardware, but tend to bulk up the physical enclosure. If you know the exact circuits you need, the whole thing can be constructed as a single circuit board or chip, which is obviously more compact and probably more efficient too. The trouble is the return on investment. If you're only building one or two of these devices, spending the time to engineer a single board to replace all the generic components will take too long and cost too much. On the other hand, it might be a necessary part of a project, if minimising size is a major consideration.
Mokalus of Borg
PS - It's generally not worth doing this for desktop computers.
PPS - Though some people do make single-board computers.