I suggest gsch2pcb to not place all components into one place one over another, but to make bounding box of the schematic and map the coordinates onto the output PCB space, with optional grid snap parameter.
This way the user knows where to expect which component and also such placement makes more sense: 1) the pads/pins are not shorted 2) the placement of components on the schematic is already logical and things which need to be close on the PCB are often close on the schematic (transistor pairs etc.) CL<
