I've been wondering why a resistor is disconnected (10K pullup) and a flat pack or discrete pullup resistors are needed with the CNC V3 shield...
Checking the schematics, I see that the SHC (Smart Hand Controller) already has the pullup resistors installed (RP1). The various Home Brew schematics do not show the pullup resistors. A note should be included in the build that states "the CNC V3 pullups are only required if the hand controller does not already include them". A better solution would be to state that "pullup resistors should be included in all home brew hand controllers" That way the possibility of "double pullups" would be eliminated
I'm not convinced that removing the 10K resistor on the CNC V3 is necessary. If it were a 2K resistor the resulting current to the MCU might be excessive but 10K provides only enough current to activate the logic circuitry, not burn it out.