‘HARDWARE>OPTIONS>Custom Boot Command’ field is only there for adding commands to the config.txt file, not for executing custom scripts.
For this, the zynthian_custom_config.sh is used.
That one is a normal bash script running at root level before the Zynthian gui is shown.
Try creating it with these commands (copy and paste them into SSH line by line:
sudo apt-get install uhubctl
cd //zynthian/config
rm zynthian_custom_config.sh
echo -e >zynthian_custom_config.sh '#!/bin/bash\nuhubctl -l 1 -a 0'
chmod a+x zynthian_custom_config.sh
The problem with a .sh script is, if you create it in WIndows, it has a wrong end of line encoding, which leads to failure of the script.
Either use Notepad++ and before saving the file, choose Edit → EOL Conversion → Unix (LF), or write the file with the shell comands from above, or use
nano /zynthian/config/zynthian_custom_config.sh
(ctrl-s to save, ctrl-x to exit) and then the
chmod a+x /zynthian/config/zynthian_custom_config.sh
via SSH. The first line of the file shall be only #!/bin/bash and then on the following lines follow your commands.