One layer needs to be embedded inside the other; copper0 inside copper1 or vice verse...
<g id="copper1" transform="translate(57.778 51.111)">
<g id="copper0" stroke="#ffbf00" fill="none">
<rect id="rect3387" height="62" width="62" y="19" x="10" stroke-width="20"/>
<circle id="connector0pin" r="27.5" cy="50" cx="42" stroke-width="20"/>
<circle id="connector1pin" r="27.5" cy="50" cx="542.22" stroke-width="20"/>
</g>
</g>