> 'guix system reconfigure /etc/config.scm --load-path=~/my-guix'

This because the shell only expands '~' to $HOME if it's a starting character.
Here you should either use

    guix system reconfigure /etc/config.scm --load-path=$HOME/my-guix
    
or

    guix system reconfigure /etc/config.scm -L ~/my-guix

-- 
Pierre Neidhardt
https://ambrevar.xyz/