yes, 'entire scene' means world position.
THREE.Vector3() has a applyMatrix4() method,
you can do the same things that the shader does so in order to project a vertex into world space you would do this
yourPoint.applyMatrix4(yourObject.matrixWorld);
to project that into camera space you can apply this next
yourPoint.applyMatrix4(camera.matrixWorld);
to get an actual screen position in -1 to 1
yourPoint.applyMatrix4(camera.projectionMatrix);
you would access your point like this
var yourPoint = yourObject.geometry.vertices[0]; //first vertex
also, rather than doing this three times, you can just combine the matrices. Didnt test this, but something along the lines of this. Might go the other way:
var neededPVMmatrix = new THREE.Matrix4().multiplyMatrices(yourObject.matrixWorld, camera.matrixWorld);
neededPVMmatrix.multiplyMatrices(neededPVMmatrix, camera.projectionMatrix);
if you need a good tutorial on what this does under the hood i recommend this
Alteredq posted everything there is to know about three.js matrices here
edit
One thing to note though, if you want just the rotation, not the translation, you need to use the upper 3x3 portion which is the rotation matrix, of the models world matrix. This might be slightly more complicated. I forgot what three.js gives you, but i think the normalMatrix would do the trick, or perhaps you can convert your THREE.Vector3() to THREE.Vector4(), and set .w to 0, this will prevent any translation from being applied.
edit2
if you want to move the line point in your example, instead of applying it to the particle, apply it to
var yourVertexWorldPosition = new THREE.Vector3().clone(geo.vertices[1]); //this is your second line point, to whatever you set it in your init function
yourVertexWorldPosition.applyMatrix4();//this transforms the new vector into world space based on the matrix you provide (line.matrixWorld)