Manual Entry vs PinPad Entry
When entering a credit card manually in the PMS, the credit card processor is unable to confirm that the card being used was truly present or not at the moment of the sale, and any transactions that are manually keyed will be categorized as "card-not-present" even if the card was physically present. This raises the possibility of a fraudulent transaction and makes higher chargebacks risks. As well, not only the processors fees will be higher but the merchant wil be liable.
When using an EMV device to use the credit card in the PMS, the cardholder had to insert the card into the device and occasionally even enter a personal pin code to authorize the transaction. If there is a chargeback, you can prove the mode of entry via your processor's/gateway's portal. The card issuer is then held accountable in this situation if credit card payments are made using a chip card and a pinpad payment terminal.