The SKR v1.3 has +5V to the end stop supply pin but a 10k pull-up on the sense pin to +3V3 (rather than +5v), which shouldn't really matter.
You don't need the divider as the CPU pins on the SKR board are 5V tolerant (when in digital mode - NOT analog mode).
Try putting a low value pull-down resistor from the sense pin (on the 3-pin end stop connector) to GND, try say 330R resistor. That should overcome the SKR 10k pull-up resistor and provide a clean 0V/+5V to the sense pin as your probe is triggered/non-triggered.
This is assuming my thinking is right with your inductive sensor having a PNP on the +5V rail that pulls up an open collector output.