I apologize if I don't fully understand your question, but the pdf
device has a "MediaBox", which is equivalent to the
"BoundingBox" in EPS
file. The PDFs from R are defined nicely using height/width dimensions,
and work well with embedding in pdflatex, etc. For example:
pdf("test.pdf",height=3,width=3)
plot(1:10)
and view the (partially binary) output in your shell:
less -N test.pdf
on line 117 of this file, I see "/MediaBox [0 0 216 216]" which is a
3in
by 3in box measured in PostScript points.
I don't understand how you are mixing this in with the epstopdf command.
If you want to make both a PDF and EPS, my best advice is to do both
directly from R (see ?postscript for EPS file generation .. the same
example as above will have "%%BoundingBox: 0 0 216 216" on line 10),
and
your output for both formats should be clean, simple, and good enough
for publishers and everyone else to use.
Just one caution, if you have a Windows computer and R < 2.5.1 (which is
most of us), make sure you write EPS files before loading up a PDF
device (PR#9517).