Discount after subtotal

You could make a custom theme, check the FAQ tab how to. Next in body.php file move below code from before subtotal to after.

<!-- Discount -->
	<?php if( $this->template_options['bewpi_show_discount'] && $this->order->get_total_discount() !== 0.00 ) { ?>
		<tr class="discount after-products">
			<td colspan="<?php echo $this->colspan['left']; ?>"></td>
			<td colspan="<?php echo $this->colspan['right_left']; ?>"><?php _e( 'Discount', 'be-woocommerce-pdf-invoices' ); ?></td>
			<td colspan="<?php echo $this->colspan['right_right']; ?>" class="align-right"><?php echo wc_price( $this->order->get_total_discount(), array( 'currency' => $this->order->get_order_currency() ) ); ?></td>
		</tr>
	<?php } ?>