Most average sized people have no problem getting a production bike to fit using the variety of crank length, seatpost laybacks and stem lengths. Custom geometry is needed for people with more extreme body proportions (upper/lower leg or leg/torso) where they need frames that are very long or short for the standover.
Tall and short riders are poorly served by the std production bikes. You can get them but the small details are missing, eg the BB height tends to be pretty fixed across the whole size range. See Zinn for why this matters.
The geometry of these production bikes is usually bodged to account for M size cranks and "normal" eg 700c wheels. The situation is getting better for small riders but its not there yet.
The size of crank is one of the starting points for frame design and seatpost/stem should be taken into account to avoid the need for extremes.
Production frames are lawyer proofed; a custom builder can go much lighter for a lightweight rider with an easy riding style. Heavier riders may need much beefier tubesets.
Custom builders can add all manner of brazeons for eg luggage, transmission(singlespeed, hub gears) , lighting. See ANTbikes, Beckman, for some fine examples.