Mini-ITX

Mini-ITX motherboards are no more rugged than their full-size ATX counterparts. In other words, they are design to run in a controlled indoor environment at room temperature and comfortable humidity. The additional PCB, however, can be designed to be as rugged as it needs to be. If you can put the mini-ITX system in a controlled environment and only put the custom PCB into the hostile environment, you still have a viable solution.

For applications that do not have any controlled environment, such as engine control for an automobile, you probably don't want to use a mini-ITX based solution.

Note that you can provide a controlled environment at your expense. A sealed enclosure with thermal-electrical cooling/heating can provide the environmental shield for the operation of a mini-ITX system. Does it make sense to use this type of enclosure? It depends. In an expensive and complicated system, you may have to do this anyway for other sensitive electronics. For cost sensitive or space constrained applications, however, a controlled environment may not be an option.