Programmers often forget how much work it takes to learn how to use their programs. Both need to be praised.
One thing that I found with PyX (and is true of many graphing
packages) is that the size (bounding box in EPS speak) of the final
graph is always different even if you give the graph the same
dimensions when you create it.
Your solution of wrapping it in a box is a
standard solution that works in many programs and in LaTeX
itself. I read that a future release of PyX will include SVG
capabilities so that we can include inkscape
drawings in our graphs. I see very powerful technologies
converging here, and this was one of the main reasons for choosing to
learn PyX.
(Given the number of number of posts to this list about preparing
graphs, both 2D and 3D, this is obviously a pretty difficult issue for
GNU/Linux users still... but it also seems that things are progressing
rapidly. Let the discussion and development continue!)