Actual manipulation of the bytecode to maintain and extend a compiled binary is wild

Just wait until you learn about machine code. :)

You'd probably use a different approach for that. Like you'd make your program dynamically load all the .dlls in a "plugins" folder -

Then you'd provide some plugin interface for the users to create plugins, for example:

public interface IImageEditorPlugin
{
    public void BeforeImageEdit(int[,] imageData);
    public void AfterImageEdit(int[,] imageData);
}

And then you can load plugin classes from all the dlls with dependency injection, and execute them though something like this:

public class ImageEditor(IEnumerable<IImageEditorPlugin> plugins)
{
    public void EditImage(int[,] imageData)
    {
        foreach (var imageEditorPlugin in plugins)
        {
            imageEditorPlugin.BeforeImageEdit(imageData);
            // Do internal image edit function
            imageEditorPlugin.AfterImageEdit(imageData);
        }
    }
}

This is a very simple example obviously, normally you'd send more meta-data to the plugins, or have multiple different interfaces depending on the kinda plugin it is, or have some methods to ask plugins when they're suitable to be used. But this way a user can provide compiled versions of their plugins (in the same language as the core application) - instead of having to provide something like lua scripts