Working through this I've realized it's probably way out of scope of ShinyProxy. I was able to manage a solution using CRIU and forking of R Markdown, Shiny, and Flexdashboard which was of course very hacky. It works outside of ShinyProxy through reverse SSH tunneling, as one normally does to access a remote Shiny instance without completely opening the ports.

But this solution hasn't been working with ShinyProxy. I can get the HTML and CSS loading but the Shiny elements fail to return. I suspect this has something to do with changing environment variables whenever ShinyProxy launches a new container.

I realize this is no longer a proper issue at this point and can probably be closed, but if anyone has insight on how to get ShinyProxy to produce instances with identical environment variables that would be helpful. Although this seems to defeat the purpose of ShinyProxy somewhat, I can see it working with user login, so I can prespec the environment for each user in the application.yml or something.