Sim, você pode especificar qual versão R será usada pelo RStudio Server. Consulte a seção "Especificando a versão R" do Servidor RStudio: configurando o servidor .
By default RStudio Server runs against the version of R which is found on the system PATH (using which R). You can override which version of R is used via the rsession-which-r setting in the server config file. For example, if you have two versions of R installed on the server and want to make sure the one at /usr/local/bin/R is used by RStudio then you would use:
rsession-which-r=/usr/local/bin/R
Note again that the server must be restarted for this setting to take effect.