Hi @simonmerrett: Happy to help. You are one of the first people (other than me) to design a front panel. Your questions will help us improve the documentation and process for everyone!
Just to help with wear, but you don’t need copper. The chassis is referenced to USB ground, and the sensor IN and sensor OUT are isolated. You do need to maintain a minimum 1 mm clearance from the screws to any IN or OUT signal. Larger clearance helps with noise immunity, which explains the rounded oval copper shape of the existing front panels.
The existing modules did not use PTH, but you can. Again, no reason for or against. The light pipe hole is not plated, so making them plated will not save a fab step. However, you could potentially plate both if cost measured in pennies becomes a concern.
Not important. You do need to plan sufficient copper (and vias if needed) for the current into pins 1-2 and 4-5. Joulescope supports 3A max with 10A bursts, so you need to consider plane resistance if your front panel supports that full range. Pin 3 is high impedance (< 10 nA current), so whatever.