Hi Tim,
I'm using the Neuron Lite and a UC400ETH (also have a UC300ETH) but have "bigger" plans for it.
Yes, at present UCCNC uses M205/M206 as the THC on/off commands from gcode. There is an output pin activated by these commands, and this output is wired to the Neurons "Hold" input. When the level goes high (5v) the AVC in the Neuron does not adjust the Z height.
The I/O connections on the UC300ETH are not "printer ports", they simply have outputs and inputs numbered the same as printer ports. The I/O is TTL logic levels (0v or 5v). I'm guessing you COULD directly wire the UC300ETH outputs to the stepper motor drives, and things would work fine. However, many people use breakout boards for isolating the "outside world" from the UC300ETH. Another purpose of a breakout board is buffering of the I/O signals.
There is a good isolating breakout board made by CNCROOM in Thailand. I think it's called the "UB1" and I beleive there is a newer UB1 in development. You should find it talked about in the UCCNC section of this forum and the Cncdrive forum (Cncdrive make the UC300 & UC300).
Good luck with your choices,
Keith.