it is cost, in the price they come you do not get all the feature, and then intel proccy are costlier too.
not putting DVD internally will save you inside space and ease on PSU, it is not that you cannot connect a DVD drive, also, I think the slim internal drives are costlier too, so why not buy a external slim burner, you will be able to boot using it and format your system.
and I do not not mini-itx boards, the ones I have given are micro ATX, also check the price of laptop HDD 500GB comes in 4K price range, if you want to minimise HDD heating you can use them instead of desktop HDD