Thanks for pinging on this! We definitely have continued thinking about this issue and a way to improve the experience on Connect. Are you encountering this issue on RStudio Connect or interactively within the RStudio IDE?
If on Connect, is the fileInput parameter working for you when you upload a file smaller than 5 Mb? Do you mind sharing what version of RStudio Connect and operating system you are running on?
If in the RStudio IDE, would you mind sharing a bit about how users get to this state? Do they just open the Rmd file and "Knit with Parameters," but are not confident with file path references and such? Essentially using the RStudio IDE primarily for its GUI-like data exploration and report generation?