It seems logical (and makes the best sense) to do the bleeding in the order described in the Shop Manual.
I do not know about later brake systems, but I could not get the brakes to feel right on my 54/55 GMC 2-ton with hydrovac when I went through the "regular"/logical non-hydrovac progression. After reading the Shop Manual and going through the procedure described, the brakes were much better. After later using a pressure filler as recommended in the the Shop Manual, the brakes were even better.
