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Saw a discussion of a similar kind elsewhere and it seems like Razorpay has a solution to this. The link to make the payment is sent to the customer's phone. Agreed, it means that the customer needs to have mobile internet to be able to use it, but it takes away at least some of the worries of having a keylogger or fake app installed on the shopkeeper's phone to track card details.
PS: I'm in no way associated with the product.