Yes, that’s certainly possible, but you wouldn’t override anything- instead you’d fetch and add the custom names when they’re registered. For a quick example, say you have an option that stores the names:
$taxonomies = array(
'ingredient_1' => 'Toppings',
'ingredient_2' => 'Sauce'
);
add_option( 'my_tax_names', $taxonomies );
Then when you register the taxonomies:
$taxonomies = get_option( 'my_tax_names' );
foreach( $taxonomies as $key => $name ){
register_taxonomy( $key, 'post', array( 'label' => $name ) );
}