I'd guess the GGP meant all of the root nodes together on one level and all of the tail nodes together on another, but single level. At least that's what makes sense to me.
This seems like it could be done in a little script in the graphviz gvpr processor.
Someone could implement this as a feature in graphviz. It might take a day to implement.
There are probably other "solutions" that already handle this more gracefully, but otherwise don't have a very complete set of features relative to graphviz.
It's reasonable (and constructive) for you to complain, but your "issue" is representative of a wide set of "issues" we've seen, and the real problem is we're just a little unimportant niche service and all this work is being done by volunteers and they mainly work on the things they know how to do.
I was thinking perhaps they want them both aligned to one side of the drawing. So for example if the direction goes from left to right, then the start and end nodes might need to be at the top.
