As someone said upthread there’s always a trade-off between how seamless the hotel wants the check-in experience to be and the risk of a chargeback. Longterm guests and elite members of the chain’s loyalty program are probably more reliable as they already have a good reputation.

In the event of a chargeback, if it is a “card not present” credit card transaction it is up to the merchant to prove that the cardholder actually authorized the charge. If the card was swiped or pin-and-chip’ed at the time of transaction, then it’s on the cardholder to prove the transaction was unauthorized, which is almost always impossible.

One time at a Design Hotel I had prepaid my reservation and at check-in they asked me to produce the card I used for my prepayment. When I told them it was a virtual card that I could not physically present they refunded my prepayment to that card and requested that I pay again with a physical card-present transaction. I’m sure they had had lots of chargebacks in the past.