I could work on core/api.php : acf_form()
// load fields
$fields = apply_filters('acf/field_group/get_fields', array(), $acf['id']);
to modify the fields keys
There is a hook in acf.php : save_post() :
do_action('acf/update_value', $v, $post_id, $f );
I probably won’t be able to prevent the product_variation meta to be linked the product, but I could ensure the meta value to be linked to the product_variation