"...would Stevenson have paired Dr. Jeckyll and Mr. Hyde in the title of his book, had he not wanted us to associate them from the beginning?"
.,,.,.

Oh, yes, why not? After all, the mystery which isn't because [see OP &c], is, just who is this mysterious Mr Hyde, whence does he come, and what precisely is the hold he has on the respectable and virtuous Dr Jekyll? In other words, the relationship between these two men is the book's subject, so why not link their names together in the title? We don't think, on reading or hearing the title, that Romeo is Juliet, or the Master is Margharita, or Mr Perrin must be Mr Traill, do we?