Using hooks is what plugin is supposed to do. Using hooks ensures that core files are not changed. Woo theme files from the theme are based on the core Woo files from WooCommerce plugin, so they share same hooks. And that is the way it should work.
Also, you can’t include files from theme into a random plugin, it doesn’t work that way. And since that YTH plugin already uses hooks, that is all OK, and no core files will be changed. All WooCommerce plugins work that way.
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