Now I've modified the rotation matrix to scale a cube into a cuboid. Below code works for me.
(I currently use no textures though;
perhaps texture coordinates are affected in some (inappropriate) manner. (?))
Thanks Egon for your quick reply :-)
box = Primitives.getCube(1f);
box.rotateY(Util.PI / 4); // cancel jPCT's default rotation around Y
Matrix scaler = new Matrix();
scaler.setDump(new float[]{
halfExtents.x, 0, 0, 0,
0, halfExtents.y, 0, 0,
0, 0, halfExtents.z, 0,
0, 0, 0, 1 });
box.getRotationMatrix().matMul(scaler);
box.rotateMesh();
box.build();
// Reset rotation matrix so above scaling is not applied twice:
box.getRotationMatrix().setIdentity();