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.
https://jsreport.net/learn/dotnet-client#pdf-utils
https://playground.jsreport.net/w/admin/kMI4FBmw
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:
https://github.com/jsreport/jsreport-dotnet-example-docker-compose