When installing through the web UI wizard, you're given the option to not install certain modules (
Customize your store -> Advanced Modules Configurations). Can the same be done with the CLI installer?
I am aware of module:disable.
There is not any option to remove specific modules during installation through cli , you can confirm it from following devdoc link - http://devdocs.magento.com/guides/v2.1/install-gde/install/cli/install-cli-install.html.
But you can uninstall those modules after installation.You can read about it in following link - http://devdocs.magento.com/guides/v2.1/install-gde/install/cli/install-cli-uninstall-mods.html