Are USB, HDMI, and Ethernet really the ports you want for your embedded system?
And by the point you don't need them, you can graduate from the dev kit and spin your own PCB without them on, if you like.
The development kit will probably break out other signals too - but if you know what SPI and CSI are, you probably don't need to be told what an embedded dev kit is :)
On your prototype devkit? Absolutely.