I can't answer precisely to your question but reading your Dockerfile, something strikes me.
CMD ["R", "-e", "shiny::runApp('.', 80, host='0.0.0.0')"]
Here you are launching your shinyapps with R and not using shiny server. I think what you want is the shiny server to render your application. Place your app in the correct folder and start the shiny server not you app with R. Then, you'll see if the configuration are correct or not. Right now, I think they are not used because you don't use shiny server.
There are several example on projects that are using images with shiny-server that you could find. The rocker shiny image is one of them
I hope it is of any help.