diffpdf is a GUI tool to compare PDF files. It has the option to create an output PDF containing both source files with differences highlighted.
The tool lacks a command-line interface, rendering batch-processing difficult. There's a patch to add a command line argument for automatic creation of an output file: https://github.com/taurus-forever/diffpdf-console
I'm just providing a Dockerfile here, combining the Ubuntu/Debian patches and the one from taurus-forever/diffpdf-console. Hope it saves you some time reading through the build instructions.
The same already exists -- didn't realize until done: https://github.com/amitev/diffpdf-console-docker
docker build -t diffpdf-console-docker .
host$ ls /home/merlin/pdf
old.pdf new.pdf
host$ docker run --rm -v /home/merlin/pdf:/root/pdf diffpdf-console-docker /root/pdf/old.pdf /root/pdf/new.pdf /root/pdf/diff.pdf
host$ ls /home/merlin/pdf
old.pdf new.pdf diff.pdf