PHP is written in text files which can be managed using any number of version control systems. Pick your poison.

https://en.wikipedia.org/wiki/List_of_version-control_software

As someone else said, you can document your patches with a Docker file, but you'll still need to track your changes.

Ultimately, what you're essentially doing is maintaining a local fork of the code and keeping it synchronised with upstream.

Instead of directly editing the server configuration, put the commands to make the edits in a dockerfile that gets performed on a newly-installed container.

I've begun making numbers of small edits to wording displayed and such across many of my applications, because I find myself engaging with multiple types of people: those with accounts, those who are hyper technical, and those randomly browsing around with no account.

I've noticed that system defaults from developers often have no bearing on my actual users, so embracing my ability to customize to taste. :)