The main component you are probably missing is dropping your customizations in an install.php file in the wp-content directory.
If you look at the /wp-admin/includes/upgrade.php you will be able to see exactly how it is included and the installation functions you can override. I am not sure if that will be good enough to catch the hook you want to use but you will probably be able to find another hook on which to “hang” your DB modifications.
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