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Well, in a way you’re right. Creating new files means you will have to stay on top of updates and see if I add anything new into those files you’re copying from and update them accordingly.
If you can use your functions.php file to inject your edits without causing issues elsewhere, that would be a great solution.
There’s really no right way to do it – it’s all preference. If you can make your DRY method work, then that’s awesome.
If not, adding template files isn’t the end of the world 🙂