Hi Strato,
Sorry for my late answer.
No, I use WooCommerce’s shipping zones in all of my eCommerce websites. I will try to explain the bug as much as I can. I have create two zones for shipping, one for All Greece’s states and one separate for Crete. I put the Crete first in order because my clients are based in Crete. In this zone, I put Free Shipping over a value e.g 50€, pickup from store and Delivery with charge.
I use your plugin to put COD on Crete and I’m watching a bug on checkout page. I have as default shipping the Delivery with charge option and COD as payment method. When I choose Pick up from store instead of Delivery with charge, woocommerce keeps the fee of CAD. Meanwhile the pickup from store doesn’t have any fees.
I hope I make you understand that I mean