No, I mean pre-process the images, but then save the changes back to a TIFF and then make a JPG copy. And use the processed TIFF to make the PDF. That way you aren't going lossy (JPG) to further lossy (PDF).
I can't speak for him, but what you are suggesting *seems* to (1) complicate the workflow (which is a real pain when processing hundred of pages), (2) introduce potential for error in archiving raw scans (oops! I accidentally overwrote my raw, source tiff with a "modified" tiff)
and (3) the end result might not be much different, if discernible at all (check out SuoerPlay's pdf's and see if the file size/image quality ratio is off base).
Personally, the toughest decision is striking a balance between quality image—vs.—file size, since lots of folks use mobile devices, don't always have the best connections/internet service, etc.
I'd love to offer highest quality pdf's....but for 100+ page magazines, the file size mushrooms to ridiculous levels.
Every 5-10 years, it seems, infrastructure improves enough that we will be able to go back to original scans and generate "better" pdf's. As phones/tablets +infrastructure improve, so will the feasibility of "super-high-quality" for everything.
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I think I got sidetracked. Ignore anything that wasn't germane.