In general, custom permalinks use native slugs by default. However, they did not have to because, as you know, you can fully customize it. You can, for example, remove the slug from the custom permalink.
Many use this feature, for example, when they want to use a numeric ID or SKU number instead of a slug. It can be also helpful when one needs to use the same slug again in a custom permalink for another post or page.
Custom permalinks are only used in permalink filters and dynamically replace the default permalinks (which are made up of native slugs). This is done programmatically, thus it has no effect on the native slugs. In other words, updating the custom permalink does not affect the native slug.
Because the function that selects the template file uses native slugs ($object->post_name), the slugs must be used in the template file names:
https://developer.www.ads-software.com/reference/functions/get_single_template/
If needed you can display the native slug inside the permalink editor:
https://permalinkmanager.pro/docs/plugin-settings/wordpress-slugs-explained/#permalink-manager-edit-slugs