Simple issue : What should I do in order to override a native js file.
In that specific case : src/vendor/magento/module-inventory-configurable-product-frontend-ui/view/frontend/web/js/configurable-variation-qty.js
If the changes you want to do can be performed using mixin, create one following the steps - https://devdocs.magento.com/guides/v2.4/javascript-dev-guide/javascript/js_mixins.html
If you want to overide and call your file instead of core file-
Place file in you theme on path i.e
src/app/design/frontend/Theme_vendor/Theme_name/Magento_Inventory_Configurable_Product_Frontend_Ui/web/js/configurable-variation-qty.js
and add the required changes.
Hope that helps.