Eunice here from the Shopify support team. Thanks for posting!
Yes, if you make a sale outside of Shopify, you can still purchase and print a shipping label from your Shopify admin, providing your account is set up for Shopify Shipping.
To be able to purchase a shipping label, you first of all need to record the sale in your Shopify admin by creating a draft order. When you're creating the draft order you'll notice that you can add a product from your Shopify inventory, or add a custom item. If you're adding a custom item, you'll need to add it you your Shopify inventory so the weight of the product can be applied.
Next, you'll need to add the customer's name and address, and then add shipping. The system will calculate the shipping rates for you based on the customer's address you have entered, as well as the weight of the product. Simply choose the shipping rate you'd like to pay.
Once you've added the product, customer address, and shipping rate, you then need to mark the draft order as paid. This will tell the system that you have accepted payment outside of Shopify and will transform the draft order into an actual order. From here, just head to the order and purchase a shipping label as usual.
I'm happy to confirm you won't be charged any transaction fees. This is because you wouldn't be using the checkout system for any sales made outside of Shopify. The only thing you will be charged for in this case would be the shipping label.
I hope this helps! If you have any questions please feel free to reach out.
All the best,