I expect this would vary based on property ownership and the requirements of their CC acquirer and or processor and not be controlled by a brand standard. Depending on the property's merchant agreement, there may be financial incentives for them to require a swipe/dip as card-present transactions often incur lower processing fees.

Requiring a physical card swipe may reduce fraud, producing and ID and the card will tend to lower incidence of claimed or real chargebacks from stolen cards; for this reason mobile check-ins may still require presentation of the physical card to be charged.

But as you said, your mileage may vary, many properties cannot be bothered to ask for the physical card.

After your stay you could contact the property and a cooperative back office agent MAY be willing to charge your stay to the correct card and refund the folio to your other card but that is fairly big ask. If you are still travelling you might consider requesting a replacement card be overnighted to your next hotel. If you indicate you know where your existing card is, but you cannot use it, most issuers will send a card with the same number.

Cheers