Assuming you have a MeshInstance3D object called meshInstance, what you need to do is apply the transformation matrix to the meshInstance's transform property. You would do it like this:
transform = Transform().from_matrix(Matrix3(1, 0, 0, -40, 0, 1, 0, -24, 0, 0, 1, 60, 0, 0, 0, 1)) * meshInstance.transform
This will scale, rotate, and translate the MeshInstance3D according to the transformation matrix.