In the end voltage is voltage; the thing is that voltage is a potential difference, in other words it’s not an absolute quality but a difference between the potential at two points in the circuit. Typically voltages in a device are considered against (aka referenced to) 0V, which may in turn correspond to ground potential. Looking at that nanosynth device you’ll see that there are points to patch a 0V and 5V from the synth. The 0V is presumably common to the sleeve contact on all the jacks: I’m not sure where the 5V goes.
Without the 0V connection there may be a potential difference between the 0V reference of the devices being connected causing what you though was 5V (referenced to the internal 0V bus) to actually be something different (and outside the allowable range) on another device. Note that that device seems to provide a bank of resistors and zener diodes to clip the voltage and limit the current. This works on the assumption that 0-5V (in fact, more likely -0.7V to 5.1V) is an allowable voltage range for the input.
Assuming you are connecting a ground/0v point on the pin patch synth to the 0V point in the breakout, or derive one from a jack on the device, your voltage reference points should match. The question is then: are the zener diodes an appropriate value for the inputs and outputs on your pin patch synth, and whatever you are connecting the jacks to (probably eurorack). If the voltage ranges work then the device will work and protect you from over voltage; if they aren’t then your pin patch synth may be exposed to harmful voltages.