Thank you for getting back to me.
After I make my corrections in Rawtherapee (and export to probably high quality jpg, but might go for the 8bit tiff, haven’t decided yet), I feed them in to another program that does some additional, guided adjustments, including “fixing” a dpi in metadata (if the metadata dpi doesn’t make sense, which is mostly disgarding outliers of less than 100, more that 9999 or just blank), splitting text from actual pictures, and a few other things and outputs a tiff for each page. That tiff goes through OCR, and then the whole thing gets sent through a pdf binding script/console program (the one I’ll probably use is written in Ruby, just in case all this matters. Image apparent size, and what the file pdf reports as the “page” size will be based on the dpi metadata in addition to pixel dimensions.
Unfortunately, my scanner (a book cradle and tripod combination) does not have a fixed lens to page distance - there are ones that do, but I had to make due with a simpler setup - so, there is some drift, if the first image is 2" x 2" and 200px x 200px, there is a little bit of drift over successive images, such that by the next calibration shot, the square might only be 150px (pulling some numbers out of thin air here, I haven’t actually checked them yet - actually, it looks to be somewhere around 30-40 pixels difference - 600 to start, 572 about 2/3 of the way through, I don’t have a calibration shot for the last page). The second step software can compensate for this, some, but I don’t know how much, yet.
Edit to add - checked the largest probable difference.
Second Edit - pre-cropping pixel dimensions are 4608 x 3456, with a lot of wasted pixels (exactly how many differs from one book to another because of aspect ratios not matching). The camera produced jpg is at 180ppi which, on a different scan that doesn’t have calibration shots with it yields an oversized printed/apparent size (16"x12" instead of the 11 1/8" x 8 3/8" actual size) once cropped according to gimp. Slightly increasing ppi/dpi in the meta will get me closer to actual size, but the second step needs at least 300dpi for text, and supposed to go to 600 for images, but I haven’t done a run to see if it makes a difference.