The basic chip design, used across a wide number of custom gate arrays, has a lot of un-connected transistors. (Chips fabricated to this level are often mass-produced and stockpiled for later use.)
Only one of the last steps, the so-called 'metal layer', which is used to connect circuitry components together, is custom. The metal layer for a paticular gate array connects together the transistors to form the desired gates, which are further connected into higher level entities such as flip-flops.
They have now been largely replaced with field-programmable gate arrays, which involve no custom fabrication (so a single stockpile can be sent for multiple uses), can be easily re-programmed during development, and can be re-programmed in the field if mistakes are found, or enhancements developed.