1) Powering a board like this with all of the add-ons is usually a problem
2) Needing that much power isn't at all necessary in the car
3) Heat generated is greater (generally)
4) Size is usually a problem for most people. Mini-ITX boards are less than 7" square...micro atx boards are a full 2.6" larger on all sides. Finding somewhere to mount that is much more difficult than a mini-itx board. Yes, 2.6" can make all the difference in the world
5) many of the mini-itx boards people are using are industrial boards, hardly any of the microATX boards are true industrial boards
If you can fit it, can power it, can cool it, and are ok with knowing that the board isn't built to the same standards as some of the mini-itx boards that many people on here are using, go for it.