The problem is that the kill switch doesn’t work if the Pi-to-SKR-USB cable is plugged in… or even touching board. It’s obviously passing 12V through my pi somehow… but how? I even tried blocking the 5V pin and ground pin on the USB-A side.
When the main power is applied, there is a converter that provides 5V to most of the circuits as well as 12V (or whatever you provide to power the system) for the motors.
The USB cable does keep the microprocessor on the SKR powered on even if the SK main power is removed. That’s what you’re seeing. You won’t be able to move the CNC as the motors have no power, but you can see the screen and the LEDs on the SKR.
So there is a jumper on the SKR that allow it to get its 5V supply from the USB. This powers stuff like the logic circuits and the CPU 3V3 power. It cannot supply motor power.
Assuming that the kill switch is the little chrome toggle switch in your photos, it appears that your switch is on the negative terminal. If so, this is most likely the problem.
The outside of the USB cable is ground, so if it is connected or touching, it is making a new.path to ground through the Pi, to the negative terminal on that PSU whivh is tied to the ground on your +12V on the SKR through the 5V buck converter. This can potentially provide full power to everything through the ground plane.
If you make sure that you are cutting off the +12V wire, this should resolve the problem (if it is what I think) it is probably best though to cut off both of the wires to the SKR with a DPST cutoff switch, but changing that to switch the positive wire will work.
