Enabling "Hardened Runtime" from outside of XCode
Are you looking for codesign's --options runtime argument? I believe that's all you need to enable the hardened runtime.

Apple has a couple of documents that make it pretty easy to figure out your own notarization flow:


https://developer.apple.com/documentation/xcode/notarizing_macos_software_before_distribution/customizing_the_notarization_workflow
https://developer.apple.com/documentation/xcode/notarizing_macos_software_before_distribution/resolving_common_notarization_issues