Best Practices: Sharing a project

Hi all- I'd like to hear some opinions and feedback on a common distribution scenario, and any expertise others might have from other frameworks or projects. Here's the scenario:

I write an app using CodeIgniter 4, post it to GitHub, it gets popular, 2000 users clone the repo, configure and run their own version of the app. They want to stay fresh with the latest-and-greatest so whenever I update the repo they merge it into their project. Well along comes some changes in app/Config/ affecting files that they have modified to run their instance (e.g. Email config, constants re-definitions, update to a third-party module config file...) and now they have a conflict.

Are downstream users of framework apps destined to handle changes by hand? I put whatever I can into environment files or the database to curb some of this, but that isn't always an option. Thoughts?