What does HackerNews think of scantailor-advanced?
ScanTailor Advanced is the version that merges the features of the ScanTailor Featured and ScanTailor Enhanced versions, brings new ones and fixes.
I use https://github.com/4lex4/scantailor-advanced to deskew the images and generate the PDF.
It isn't perfect but my purposes are more around research than publication, so, YMMV!
Scan Tailor forum: https://forum.diybookscanner.org/viewforum.php?f=21
Also, almost all such watermarks would be easily destroyed by bitonalization and despeckling, which is usually done anyway to reduce the file size (e.g. it's part of the default operation of https://github.com/4lex4/scantailor-advanced ). Arguably the same is true for yellow dots if one is leaking scanned printouts, but identifying leakers is not the main purpose of the dots...
If one really wanted to, one could try embedding little holes into certain letters and hope they survive the smoothing algorithms and don't stand out too much. Not sure how successful that would be, though.
https://github.com/4lex4/scantailor-advanced
I find the autodeskewing algorithm to work well, but it allows hand adjustment as well, which I like. As I've gotten better as using it, I've been able to get the size of my scanned documents down considerably by cleaning up the scans. This includes some old manuals.
As far as the pdf encoding itself, I use both mutool, from mupdf, and qpdf. I just checked and it looks like while they both compress their streams, it may not have the same flexibility with Acrobat Pro. For me, I'll decompress, edit, and recompress streams on the files and that's been fine for my use.
That said, if someone knows of a better tool for compressing streams in a PDF, I'd be interested to hear about it as well.