Hey Forrest,
if I understand you correctly, you want that normally the milling motor and the dust extraction are switched on and off by the CNC controller, but you want to be able to get manual control over them at any time, is that right?
What I don’t understand then, is why you need a microcontroller and a home automation server to do this. This seems to me like chartering a A380 to visit your neighbor to have a beer in the house next to you 
. I think all you need to make this happen is two relays and a few DPDT switches (and two LEDs if you like).
Please don’t get me wrong, I am someone who thinks about things you can do with microcontrollers every day. But I would not use one if i can accomplish the task more easily in another way. I can think of more demanding tasks for justifying the use of a microcontroller.
- @Satoer uses a microcontroller in their Control panel, but here it emulates all the keycodes that the gamepad sends via USB.
- Branden @WildMtnCraftworks uses a microcontroller in his Journeyman Enclosure With Utility Room, but it is to capture a range of operating conditions like coolant temperature, VFD alarm states, etc. and to drive a Nextion Human Machine Interface Display which shows a lot of information about the entire (VFD/spindle-based) CNC system
Can’t you can simply connect two relays to ‘tool-enable’ (pin 15), so that the devices are switched on and off by the CNC controller, and bypass the state of the relays with two switches, if you want to control them manually?