Yes, this is a tricky question that draws on a less commonly known aspect of how enzymes work, although when you think about it, it's logical that they will have a very high affinity for the transition state. (The Wikipedia article on transition-state analogs
is interesting reading in this regard). To answer your specific question, though, the correct answer states that the researcher would develop a molecule that resembles
the transition state, which is not quite the same as stating that the transition state is
a molecule. In general, MCAT questions will tend to be worded in a way that sidesteps thorny theoretical/philosophical issues like the precise nature of a transition state.
Hope this help clarify things, and that your studying is going well!