A:AnswerYou should have no problem fitting a mATX (Micro ATX) board into this case. I've got a Asus B350M-A (Micro ATX Board) build and it fits perfectly fine!
A:AnswerIt comes with a USB port on the top of the computer, the other USB ports will depend on what type of motherboard you put in. As for HDMI and any other displays, that will depend on what type of graphics card you put in the motherboard. This is only a case.
A:AnswerThis isn't an all-in-one desktop. This is a PC CASE to put all your parts in. You probably see everything in total for $600 because you're looking at the tab where it says customers also bought it with which isn't necessarily a requirement.