So sorry for the trouble here. Unfortunately, I believe that this is still broken and does not have a solution yet.
Did any of the workarounds or solutions proposed here seem amenable to you?
In particular, my latest meanderings lead me to imagine a workflow like the following:
upload file to Shiny app
Shiny app pins the file
Shiny app renders an Rmd pointing to this pin
Shiny app redirects user to the rendered Rmd
There are some tricky bits of this workflow (namely, how to get the Rmd to point at the pin, how to give the user access to the report, etc.), but I am inclined to try a little prototype if that workflow would be helpful!