Unfortunately, it works as you observe. The chrome bundled in jsreport.Binary.Linnux doesn't inject pageNumber in docker. I haven't found what is the actual reason for this. It could be an internal deps version mismatch, but I couldn't verify it.
What you can do is use pdf utils to merge footer with page numbers.
The other option is to boot the whole jsreport in the next docker container and communicate with it with jsreport.Client nuget. This option typically scales the best. Example: