Honestly, this type of board is something that you aren't really going to just install in a case and forget about it. You are most likely going to have this on

Honestly, this type of board is something that you aren't really going to just install in a case and forget about it. You are most likely going to have this on a test bench so you can swap out all kinds of different hardware for validation. Buttons on the bottom for power/reset, 2 different JTAG ports, DIP switches for settings, and remote board management aren't things that are normally found on consumer boards. Mini DTX probably allows them to have a marginally smaller width compared to Micro-ATX while still allowing space for all of that debug functionality with a 2 slot graphics card installed. eMMC is also kind of important for a SOM as well.