The Bookmarks aren't all that useful. Were they done automatically?
You can edit them with jPdf Tweak so that proper navigation will be possible.
I also recommend putting something like
> Mirror of YuYuHunter's translation of Philipp Mainländer's works as of 2018-07-30 > > https://reddit.com/r/Mainlander/comments/5r8wn2
at the bottom of the cover.
The Letter was not done by YuYuHunter, so you should credit it's translator on it's respective page.
The utility jpdftweak (java based), can resize all pages instantly using its Page size Tab. It can scale to a wide variety of preset sizes, more than you'll ever need, and changes all pages to that size.
Download: http://jpdftweak.sourceforge.net/
If you are still looking for a solution, I think I found it with jpdftweak (http://jpdftweak.sourceforge.net/).
It is java-based, and really non-intuitive, but it works. Look at the manual page on the web site.
To make 4 pages per fold, go to the Shuffle/N-up tab, tick Shuffle Pages, Choose the preset: Booklet Reorder then tick "Shuffle blocks of" and put in the number 4
Choose an output file name and click Run. It is a bit slow, but it works.
JPDFTweak can do both of those things and I regularly use it for that, but it's not the most intuitive thing ever. But source seems to be on website: http://jpdftweak.sourceforge.net/
It's the pdf page labels you're wanting to edit. jPDFtweak can edit them and it's free, open source too I think (http://jpdftweak.sourceforge.net/ ). It's much less intuitive to use than Acrobat though.
I use jpdftweak and it works pretty well. It also helps me change page numbers to an offset (Cover, i-v, 1-256, etc.)
Really useful for pdf reference books that I want to keep on my laptop.
>Compressing and merging are the most important factors.
Take a look at jPdf Tweak. I'm not sure if it has CLI or not. Also search for the 'pdf' tag in Software Recommendations Stack Exchange