I've chose to do a normally closed setup for my limit switches as well, for the reason for safety, any broken wire should also halt the machine. Much like real world alarm contact or fire alarm trigger. Based on the note from https://github.com/grbl/grbl/wiki/Configuring-Grbl-v0.9
I really don't see the purpose of a pull down resistor here. The limit pins are grounded in normal state, and the internal pull up will bring it to "1" when the switches activate, having a pull down will essentially becomes a voltage divider and resulting in 1/2 VCC if the resistor value matches. Unless the note is referring to wiring the common to VCC which means no invert is required for normally closed setup, unless it's a normally open setup.NOTE: If you invert your limit pins, you will need an external pull-down resistor wired in to all of the limit pins to prevent overloading the pins with current and frying them.
If someone can help confirm that, then we should correct the note to avoid future confusion.
Btw, I'm actually PIC guy, so no idea if prolong grounding of a pulled-up pin of AVR will cause any issues or permanent damage to the MCU? I can't seems to find relevant warning on this.