Why was an auxiliary verb put in front of the sentence? Also, was the subjunctive used in this particular sentence?
The sentence doesn't actually start with the auxiliary verb "had." It actually starts with "and," which unfortunately not said in this particular fragment. The entire sentence is "And, perhaps the kind of life that she has led could have been a very similar life to his, had he not ended up walking the path that he did." Even though "and" is a conjunction, you can use conjunctions at the beginning of the sentence. As for your second question, I believe that you are correct about this being the subjunctive mood. This is because he is making a statement that is contrary to fact; that Enola could have ended up like Sherlock Holmes.