Factory pattern versus dynamic class instantiation in PHP

Question

I am developing a web framework in PHP, and I want to make it fully extendable. My goal is to make it possible for a developer to change the behavior of any component without having to modify the "core" codebase at all. Developers should be able to encapsulate all of their work in a separate directory. And, I want to do this without using "hooks" (i.e., event listeners), which can quickly turn into a huge mess.

For most components, I have this figured out:

• The Pimple DI container allows you to extend existing services.
• I'm using Twig as my template engine, which allows templates to be overridden.
• Front controller routes can be overridden by redefining them.
• I'm using an extendable uniform resource locator to allow developers to override or add search paths for resources (assets, configuration, schema, etc).

The problem I face is extending the functionality of a class when there are places in the core codebase that already instantiate that class (because my framework is a full-fledged application rather than a library, even with IoC, I still need to instantiate the class at some point).

Inheritance alone won't solve this problem, because I'm still instantiating the base class in my core controllers/routes/whatever. It would seem that I need to introduce an additional layer of abstraction.

One idea I have is to just use PHP's dynamic class instantiation feature. For example, if I have a base User class, and I want to allow developers to replace all instances with a CustomUser class:

// In a config file (which *can* be overridden) 
$userClassName = "User";

...

// Anywhere I need a User, or User subclass: 
$user = new $userClassName(...);

Now, a dev simply needs to override the value of $userClassName and set it to the name of their child class.

Alternatively, I could wrap this all in a Factory pattern:

class UserFactory
{
    public function createUser($type = "User", $args)
    {
        return new $type($args);
    }
}

The advantage of the Factory class would be that I could do some type-checking, but then I'd need a separate Factory for each base class.

Are either of these approaches the right way to implement this kind of extensibility?