Display Customer order comments (customer note) in Woocommerce
Ok, after some time spent on trying, I finally find out that the right way to display the customer checkout comment is selecting $order->customer_message; and set this value as variable.
Update 2017 - 2018 | For Woocommerce 3+
Since Woocommerce 3 you can't access anymore properties From the WC_Order object. You need to use the WC_Order method get_customer_note() instead:
$customer_note = $order->get_customer_note();Related:
Display order customer note in Woocommerce email notifications
Add order customer note to YITH Woocommerce PDF Invoice