I know there were a couple of replies to this, but they seem to have vanished (at least temporarily) with the new forum. I’ll try to address what I remember of them.
Pdf is the final form for this user manual. It used to be maintained in MS Word, but due to a combination of its size and the large number of images and cross-references, Word would periodically corrupt it. (It probably didn’t help that multiple people were editing it.) The last time that happened, I recreated it in Scrivener, thinking that its cross-platform availability would make it a good solution, rather than try to patch it up in Word again. I could in theory tell Scrivener to compile to some other format and generate the pdf from there, but with the references being messed up, that won’t work.
I know that it is possible to create internal document links in a pdf on Windows. MS Word, LibreOffice, LaTex, and the pdf editors that I regularly use all do it. I don’t know what pdf package(s) Scrivener is using internally, but those links seem to be basic functionality elsewhere, and if Scrivener can’t do them, that’s a show-stopper.
Regarding path differences between MacOS and Windows, all of my relative paths are perfectly valid on either system, as long as the separator ("/" vs “\”) is not an issue. I tried changing the separator on one of the images, but Scrivener still didn’t include it. One of the currently missing replies mentioned the possibility of using compile-time replacements to swap in the correct absolute path. I just tried replacing “./_img/” with the absolute path, and it does at least find the images now. Unfortunately, it’s not formatting them correctly, plus I couldn’t put this out with all the internal links missing even if the images were perfect.
To further complicate things, I replaced my Mac with a Windows box when the Mac started having hardware issues and it wasn’t clear if Apple was about to make it completely unusable for audio recording. I still have the Mac, but I don’t know if it will work the next time I turn it on, and I certainly can’t expect to use it for compiling Scrivener docs going forward. I have a Linux box, but my understanding is that the unofficial Linux version is the Windows version compiled for Linux, so it probably wouldn’t fix any of these issues.
Since my original Scrivener purchase, I have successfully used LaTeX for some other projects, and I suspect that will be the way forward, either starting from the TeX compile that I did a while back on the Mac, or just copying everything out of Scrivener.