Your first step should be to run the RetroCRT tool & update it, then run it again via the RetroPie screen in EmulationStation.
Use RetroCRT's bug tracking page or join the Facebook group and post there.
You're not changing the horizontal resolution before starting the emulator, this is an issue with the /opt/retropie/configs/all/runcommand-onstart.sh script.
RetroArch is ignoring our custom_viewport_width setting, and probably the height as well.
You'll need to update /boot/config.txt and set the following to 519 for RetroTink & 0 for all other platforms.
dpi_output_format=0