Conditional Shipping & Payment Methods

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The problem below has been mentioned numerous times here on the forum, but no one gave an explicit solution to that.

We are looking for a native solution to address the Conditional Shipping & Method issue without using any external paid plugin etc..


Our shop has two primary shipping methods: Pay on delivery which is cost more, and we have the option to ship the products and pay beforehand (Like PayPal, bank account, etc) 

Issue #1: Customers are using as a Shipping method: NON-PAY ON DELIVERY  (which costs less than pay on delivery) and when they jump into the next step which is the Payment Method they are choosing to Pay on delivery. (So every time this scenario happened we have to follow up our customers to explain such and such) 

So what they achieve with that?

#1 They pay less than they should, and this has, as a result, our company to lose money on every single order.
#2 Also we have to deal with it over the phone and this process is time-consuming.

We are expecting to have this functionality on the Shopify.

Thanks, waiting for your thoughts on that.