How can one respond to the evidence presented from the Quran and Sunnah, specifically the verse: "Their mark is on their faces from the trace of prostration," which is used to argue that prostrating on earth is a right and leaves a clear mark on the face, based on the interpretation of the apparent words and meanings of the verse?

There is nothing in the Qur'an that indicates a prohibition against prostrating except on dust. What was mentioned in the question, if it were true, would be evidence for the desirability of prostrating only on dust. Ibn Taymiyyah reported the consensus of the scholars on the permissibility of prayer and prostration on mats made from materials that are of the earth's kind, such as straw mats. He also mentioned that most scholars permit prostration on what is not of the earth's kind, such as carpets and rugs, and this is the view of the people of Hadith (definition) and the people of Kufa. He cited as evidence for this permissibility the Hadith of Aisha that the Prophet (peace be upon him) used to pray on a mat that was not of the earth's kind. It was also narrated from Mughira ibn Shu'bah that the Prophet (peace be upon him) prayed on a straw mat and on a tanned hide. Ibn Qudamah stated that prayer on straw mats and carpets made of wool, hair, animal fur, clothes, and all other pure things is permissible.