It would be nice if we could input some WP-CLI commands of our choosing alongside the WordPress pre-install options when setting up a package. Initially, I wanted the ability to pre-install custom plugins that are not listed in the WordPress.org directory, but I figure that letting us instead run our own WP-CLI commands would give us more flexibility to configure the pre-installation of our WP instances exactly how we want them, since WP-CLI is a powerful tool that lets you fiddle with almost any WP option you can think of.
This WP-CLI commands to be run would be setup at the package level when chosing to pre-install WordPress in the package options. Ideally, I think the WP-CLI commands should run once WordPress is done installing.
cPanel already has an option like this in their WP Toolkit, if I'm not mistaken.