First, we agree that we could improve the current layout for nwdiag.
However, it's not that simple.
Somehow, we have to align boxes because it greatly simplify box connections.
We have added a slight shift to avoid too straight lines, but it's clearly not enough.
I suggest that we work on some complex example, something like:
Maybe you can use any image editor to manually edits links so that we see how we should draw this example.