I opened Onyx and searched until I hit Parameters > Finder > Finder Menu > Show Quit Finder, which was enabled (apparently by default)...
Not by default, no. OnyX reads the
current state of each of those parameters, then displays those states as the presence or absence of checkmarks in the relevant checkboxes. So when you launched OnyX, the app noted that the Finder Quit menu item was
already enabled on your system, and thus displayed a checkmark in the checkbox.
Otherwise—if OnyX applied a set of default parameter values whenever it was opened—you'd have to go through and reset all multiple dozens of them (or however many you'd changed from the defaults) before closing the app, or all your preferred tweaks would be undone.
