مُتَحَرِّكَ الْأَوْسَطِ concerns the vowel on the word’s middle letter, not the case ending imposed at the final position.
In شَتَر, the middle ت is vowelled; in نُوح, the middle و is sākin.
By contrast, the kasra on the final letter of بِنُوحٍ is a genitive ending. Keep these two concepts separate.