Hi JD - sorry I have taken so long to respond, one of those days when I get started, then something pops up, continually.
I had a look at your project, yes, your .Rprofile is visible to me, and executes when I start the project ("Hi!"). I think this is a project-based .Rprofile, rather than a user-based .Rprofile. FWIW, I just started using RStudio Cloud yesterday, so I don't think it's a version-issue.
Let me return the favor, by setting up and publicizing a project, but with the .Rprofile in /home/rstudio-user.
I'll post again soon!