You find the relevant code in the mentioned PR. For example the following matrix:
var matrix = new Matrix4().set(
1, 0, 0, 0,
0, 0, 1, 0,
0, - 1, 0, 0,
0, 0, 0, 1
);
is a so called change-of-basis matrix. It converts from right-handed Z-up to right-handed Y-up. You can convert a given local or world matrix of a 3D object like so:
var matrixInverse = matrix.clone().transpose();
object.matrix.premultiply( matrix ).multiply( matrixInverse );
This approach also allows to convert from left to right handed coordinates systems (and vice versa) with arbitrary up directions. It’s just a matter of how you compose the change-of-basis matrix.