Given you have said they haven't yet made you an offer, in my mind there are two scenarios, depending on how you are feeling about the position:

If you *know* that you no longer want the position, based on what you have seen so far, then you may as well withdraw your application, as there is no point in wasting further time on it. However, I don't think you would have a lot to lose by waiting to see what their response is to the interview. You can always turn the position down at a later date. Once you have withdrawn, there is no going back.

If you think you *might* still be interested, based on the potential answers to your questions, my advice is to wait until they respond, before you fire your list of questions over to the Hiring Manager. Because, if they don't want you anyway, then you will be wasting your time and these questions will be academic. Besides, they might offer you another interview round, in which case you may yet get a chance to ask your questions in person (and seeing their body language may give you additional useful clues).

If they do give you an offer, then you can write an e-mail to the Hiring Manager, stating that you like the position and think it is a good fit; however, you have some questions that you would like them to answer, before you would accept.