Best Practices: Sharing a project

Depending on what type of configuration you need to save. It can be done in the database itself (if the app are database driven).
Or save a file during configuration/initial setup. Most apps that I download requires you to copy the sample Configuration file, and make it your own. And therefor it will not be overwritten. But they will not get the latest goodies (in terms of new configurations). That conflict will they need to solve on their own.

You should of course hint in the changelog and/or upgrade guide on new configurations options so they can copy those over. Personally I make this file read-only so it can't be overwritten, so I don't appreciate someone trying to auto-patch it.

I would also include CI4 with Composer, the framework itself. So that they can (if/when) you abandon said project. Always be able to download the latest CI version instead of downloading a zip and patch it manually. "Adding CodeIgniter4 to an Existing Project". It will also slim your project down. If you have a specific version in mind. Specify it in your Composer.json instead.