"Isn't that machine small?"
Translation:Není ten stroj malý?
Ten is masculine nominative (both animate and inanimate). Also, the machine is the subject here, that's why it is nominative.
It also comes after the noun in English in this case.
It has to do with its use in the sentence, instead of "small machine" and "malý stroj", we are talking about whether or not "the machine is small" or "ten stroj je malý". The rules about adjective placement relative to their nouns refer to the situations when they are being combined into noun phrases (a small machine), not to clauses in which they are separated from each other by intervening elements.