Your matrix in the example is correct. The paper says
σ1≥σ2≥…≥σn≥0 and establishes thus an order for column 1 to column n this way. I would bet that the reverse order would work as well as long as we use the reverse order of column vectors in the matrices, too. But "filling up the rest" is much clearer than starting with the arbitrariness in this rest and administrating the size of this rest only to begin with it. Remember that we had
u1,…,ur and any orthonormal complement for
ur+1,…,un. Now imagine writing: Start with an arbitrary orthonormal complement
u1,…,un−r of
un−r+1,…,un, etc. That would probably work, too, but would be much more inconvenient.