For some reason, the Helvetica fonts tend to be clipped
This is most visible in the italics.
My guess is that the genfonts tool is not correctly
handling the bounding box---but I can't see where
genfonts is in error and the other fonts all are handled
The best way to handle this is to fix genfonts, as we
(or users of the library) may conceivably want to
regenerate the existing fonts, or generate new fonts.
(One very likely reason to want to regenerate the
existing fonts is for Unicode support.)
So, hand-tweaking the glyphs is not really a good
solution, unless the X server's fonts are just
inherently broken. I do not believe that the X server's
fonts are broken.