SBC

Most SBCs come with some control interface circuits. For example, the Z-World OEM2500 has two PWM output, 8 digital inputs and 8 200mA capable outputs. If that fits your need, you don't have to do anything.

On the other hand, if your application requires to switch more than 200mA, you have to design your own PCB. If your application requires one or more H-bridges (for motor control), you need to design your own PCB. If you application requires high precision ADC ability, you need to design your own PCB.

SBCs are great when you don't need any more than the provided features. As soon as you need any more than that, however, SBCs do not offer much advantages of mini-ITX motherboards.