In this case, the additional charge is imposed by the bank, not Agoda.
If you display Agoda in THB and choose to pay in THB after keying in your card info, Agoda will charge the exact amount showing on the website. As an example, if you use DBS Visa Debit Card linked to a MCA account with enough THB balance to pay, you will be charged exact same THB amount, and will receive 2% cashback in the next month, provided the conditions for cashback are met (minimum spend of S$500 on Visa and cash withdrawals limit of S$400 and below in the same month).
This is a good way to 'clear' foreign currency balance in your MCA account, or clock spending for credit card sign-up bonus if foreign currency spending is required (e.g. CITI Prestige).