Also, if you include miniDP and don't include HDMI, you don't have to pay the HDMI licensing fees.

Many of these SoC have HDMI directly from the IC without needing additional hardware converters. Something like DP you need a converter IC which adds expense and board space/complexity. Something like MIPI -> DP, I think TI makes some chipsets that do this.

The size is probably to save space on the board - looks like they try to keep to relatively the same size and mounting holes as previous boards.

I have an entire box of these mini-normal converter cables because of boards like this. OK when messing around but I can see the frustrations if you're not used to it.