Using an offscreen scene to pick the scene coordinates matching the map coordinates ?
Maybe using Context.prototype.pickValue() is applicable for getting coordinates of the first surface seen on top https://github.com/x3dom/x3dom/blob/87a5c8575948cc07a3c9b28963e77a65ddbb9f71/src/gfx_webgl.js#L2888 (eg: playing with viewarea, viewMat and sceneMat, and setting the 2D coordinates to 0,0)