for pdf mode there are only two occurrences of \pdfdest (red and green), while for dvi mode there are three occurrences of setting destination marks (red, green and blue). I would like to point out
that in pdf mode there is \makebookmarks macros, which does the same job more clearly, than it is done in dvi mode.
in dvi mode link to first section points before date, not before the section itself, as in pdf mode
The patches in the attachment show the effect of using colored boxes instead of destination marks.
Take latest cwebmac.tex (ver. 3.69) and test.w from the attachment.
First apply patch cwebmac-dvi.patch:
Then apply patch cwebmac-pdf.patch:
Now compare test1.pdf and test2.pdf
I see two problems: