It's up to you which way you want to do it. You can either add your own hooks into that file, or just add your own code into the file. It's a matter of what you like better. For instance, I wrote a tracker integration product for our site and had to insert some code into a file where there was no hook. I choose to add a hook so I could have all the code right there in my admin panel to change. However, when I choose to make a change in our external.php file, since it was for a single purpose and not related to any plugins/products, I decided to just change the file.
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