First, you have to make sure both are compatible. If they are, the fsb will just be at 800 instead of 1066. This is not a big deal for a carputer.
Intel makes mini-atx boards that are 1333 fsb for the new core 2's.
Carputers are usually slower, older technology. They are not usually the latest and greatest, therefore the mini-itx motherboards which are designed to be used for things like carputers, firewalls and other low power applications are not the latest and greatest.
If you really want to have 1066 or 1333 FSB go with the mini-atx board, not an itx.