Three.js – How to pre-position objects to merge?

I’ve successfully merged my cubes, although they seem to merge together reverting back to their original position/rotation, ignoring the declared positioning/rotation

var geometries = [];

cube1.position.set( 0, 0, 0 );
geometries.push( cube1 );

cube2.position.set( 1, 0, 0 );
geometries.push( cube2 );

cube3.position.set( 0, 1, 0 );
geometries.push( cube3 );

const cubes = BufferGeometryUtils.mergeBufferGeometries( geometries );

scene.add( cubes );//All the cubes get merged on 0, 0, 0 - overlapping one another

How do I position the cubes so they can be merged in their declared positions?