I don't understand why you think there should be an Emulationstation folder in you $HOME after you install the package through the RetroPie-Setup - the installation folders for all packages are in /opt/retropie. After installation, you should be able to start Emulationstation using the RetroPie shortcut (.desktop) file added by the installer.

@Clyde You could add the info to an existing issue or open a new one, but I'd test before using a 'standalone' RetroArch (they provide 'flatpak' packages to install easily the latest version) and maybe modifying the build script in RetroPie-Setup to get the latest version of RA to compile.