That's fine. I can shuffle the pins around somewhat without much effort. There are just a few limitations that have to be adhered to:
1) The 4 LEDs must be on PWM capable pins (they have little white circles around them on the silk screen in the picture I posted)
2) The X, Y, and Z accelerometer inputs must go to analog inputs (A1, A2, etc.).
3) Clash sensor must be in pin 2.
If you make the PCB just ignore the AXDL335 VDD and VCC pins on the arduino, that's fine; my software will still work if it's powered more directly by a 3.3V power rail. If the accelerometer pins are left as is, you could just map the X, Y, and Z inputs to the module and ignore the ones I'm using as power pins, don't give them a trace at all. That way the module could either be piggy-backed on the arduino or use your board's mapping. It also opens the door to making a shorter, simpler version of your PCB with no mapping for the accelerometer pins at all, assuming it would be piggybacked.
The accent LED is for lighted switches or indicator lights. In my videos, that is the output that is controlling the blinking of the LED in the ring switches that I use. It's an optional indicator light.
Thanks for the heads up on the PWM markings and pin designations, forgot they were fixed position.
I'm always looking for ways to make my boards smaller and Bill's genius stack gave me an idea (thanks Bill

). I've had a play with some strip board and various headers to find a workable arrangement. I hate making circuits with strip board but I do use it like lego for working out physical dimentions and arrangements.
Size wise, it would fit hilts with a minimum ID of 28mm if the headers are used in the regular fashion. However, it would be possible to lower the depth by modifying some of the male headers mid assembly and mounting one or two modules flush to the board (the pro mini and WT can both do this as there's no surface mount components on the flip side of them).
As to the layout I'm reworking now, I've used the Spectrum as the template as it supperts upto 6 LEDs. Here's what the pin list looks like:
2= Clash sensor
3= NFET gate1 (FoC LED)
5= NFET gate2
6= NFET gate3
7= PWR button
8= AUX button
9= NFET gate4
10= Accent LED 1
11= Accent LED 2
12= BUSY
13= SCK
A0= X
A1= Y
A2= Z
As it didn't seem likely that anyone would want to change the white LED for a different colour, I've opted to include an SMT resistor on the PCB for 1,2 and 3w setups and resurved output channel 1 (gate 1) exclusively for the FoC function since the LEDs Vf and power ratings will be a fixed point.
The other three LED output channels have been left resistor free however. Regular resistors will need putting in series with the LEDs in the usual fashion but setting it up this way allows the PCB to suppert custom and regular colour swap outs regardless of voltage or watt.