All these values are described in full in the scad/ README. Other parameters such as wire/pin diameters and pcb/plate thicknesses (and many many more) are contained in parameters.scad. Once the basic layout is set there are more values you can tweak in layout.scad to change the footprint of the PCB, add components like MCU/TRRS sockets, and add stabilizers/standoffs. The OpenSCAD script reads the layout data from the layout.scad header file, which you can either write by hand or generate from a KLE json file using the provided script (requires node.js 14+):
3D-Printable Hotswap Keyboard PCB Generator