slim4-skeleton VS clean-code-php

You can have the container call in a config folder with a file called dependencies or how ever you want. A few existing examples of this is here - Slim calls this app/dependencies in this skeleton project and Odan's Skeleton has this as config/container in their project.

Yes, as an example, the First Application's business logic (not that it's much) doesn't tie itself to the framework, as one example. Odan's Slim Skeleton, ADR Example (yes, I know you are the author), and the Aura Payload example class can be seen as other examples.

Even just the tests in your first link are very useful to see, such as: https://github.com/odan/slim4-skeleton/blob/master/tests/TestCase/Action/Customer/CustomerCreatorActionTest.php

Another option, to me and speaking to the OP as an alternative, it is simpler to add some Data Mappers/Repositories to abstract away the Database code. Good examples is the sample ADR application, Payload library example, Slim 3 First Application, or this Slim 4 Skeleton application

You could also use a Slim Skeleton like Odan's which incorporates much more features to help - docs.

Try Slim again. The setup may be too much, but the concept is the same. Look at the first application or any of the skeleton apps to help (https://github.com/odan/slim4-skeleton for one).

More clean code concepts from this GitHub repo. Derived from Robert C. Martin's book Clean Code, adapted for .NET/.NET Core. There is also for JavaScript and PHP.

“Clean Code” concepts adapted for PHP

Clean Code PHP - https://github.com/jupeter/clean-code-php

Clean Code PHP

- Clean Code PHP - Examples of good and bad habits/standards to use in your code

My recommendations are starting learning about clean code, and put in practice here are a guide PHP clean code.