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When unit class is using for very small values like mm or um, there is a problem because resolution values in the postscript file are too small.
A better way is to use the scale command with "x y scale"
In principle, you are are right, but this cannot be implemented in such a way in PyX.
PyX deals a lot with these coordinates internally and cannot keep track of these scaling
informations up to the point where the output file is created.
Thanks for reporting anyway, and sorry for the long delay in answering to this query.