What does short circuiting a RST front IO header do?
You are wise to ask.

The safest option is to use some means of isolating the two circuits from each other. The standard methods are relay and opto-isolator.







simulate this circuit &ndash; Schematic created using CircuitLab

Figure 1. Relay isolation. Figure 2. Opto-isolation.

Relay


When GPIO goes high Q1 is turned on, RLY1 turns on and the reset contact closes.


Opto


When GPIO is pulled low D1 turns on. The light hitting the base of the transistor turns Q2 on shorting out its collector and emitter.


With either of these arrangements the two systems are electrically isolated from each other and a fault on one won't affect the other (other than, perhaps, the Pi shutting down the MB).