This is solid advice. If you are really planning on compound turbos and high boost, and you are going to go through your 6.9, you should have the machine work done to the block to accept the larger studs that the 7.3 came with.
Has anyone ever successfully done that? I know you can't just drill and tap (something about the 7/16 Major diameter being larger than the minor diameter of the larger studs) so I'm assuming that would require either helicoils or threaded inserts.