That's right. There are concepts such as multicurrency conversion, but these situations are rare enough not to be a concern for most travelers. I've only personally come across this with VAT refunds with Global Blue.

There are destinations where there's a local currency but transactions are primarily in another currency. Two such examples are the Cayman Islands and Aruba. Unless you have a local card, payment processors will process credit card transactions in USD, regardless of the currency denomination of the card. Menu prices in the Cayman Islands usually reflect a KYD price with 1 KYD = 1.25 USD even if the official exchange rate is 1 KYD = 1.2 USD. In Aruba, most menu prices where tourists would be are denominated in USD. Some show AWG at the official exchange rate and others show < 3% markup to USD. However, these are all disclosed before you give payment, so, like with your examples in Jordan, you can decide if you want to pay cash or whatever the merchant decides the USD price would be if making a card payment.