The motherboard tray has several cut outs for routing cables. None of them have grommets, though.
The motherboard tray is held in place with four (4) screws through rubber spacers.
The motherboard tray can be removed.
The screw stand offs can be reversed, and the motherboard tray can be mounted reversed, if you wanted a tech bench type set up. Not sure if they intended it to be this way, but it does work.
After installing the included motherboard standoffs, you can mount an ITX motherboard, with the I/O facing up (towards the handle).
You will have to remove/replace the expansion slots to fit ATX (and be mindful of the I/O being blocked by the frame), but you could easily fit a Micro ATX motherboard if you drilled your own holes for stand offs.
An ATX motherboard even fits with the same conditions as above.