You can allow multiple sku’s just by deactivating the sku unique check from WooCommerce. To do so, just add the following line into your functions.php:
add_filter( 'wc_product_has_unique_sku', '__return_false', PHP_INT_MAX );
How i came in contact with
I have used this in a Project where i’ve used Polylang. WooCommerce was shouting because the translations had both the same sku. After adding this, i had no problems at all. Because of this i would recommend it to you.