That project is super expensive for the quality of the product. I have built myself a CNC router capable of producing PCB, cutting wood and acrylic for about 1900$ with a bigger cutting area (12"x18"x3"). I bought a Fireball V90, added some powerful stepper, a Bosch Colt router and a few others things and the price is still cheaper than that kickstarter project.
This project is also using 1/64" endmill, so the minimum clearance excluding backslash and runout is about 16mil. Those endmill are quite easy to break and quite expensive, he is probably using these because these work fine if the PCB is not perfectly level. A V-shaped tool is a lot cheaper and can produce 10mil clearance without problems if the depth is probed/measure before cutting. My CNC probe the PCB at regular interval and adjust the depth when the program is running so a cheap 2$ v-bit is able to etch the PCB at the right depth across the PCB surface.
From what I can see in the video, he is using pcb-gcode, a free plugin for eagle, to produce the Gcode used to control the machine.
/end rant but I could easily continue...