Must the movement of the tongue in silent prayer correspond to its movement in audible recitation, such as the tongue touching the roof of the mouth for the letter “Raaʾ,” or is that considered extremism?

The letter Ra (ر) is pronounced from the tip of the tongue with the gum of the upper incisors. Your statement "upper throat" is incorrect, as it is not one of the guttural letters. If the tip of the tongue does not touch the gum of the upper incisors, its pronunciation is incorrect. There is no difference in the pronunciation of a letter between secret and audible speech. The letter should be pronounced without exaggeration or extremism, as that is blameworthy and leads to obsessive doubts (waswasah). Therefore, you should repel these doubts and pronounce the letter in secret just as you pronounce it audibly.