The main two things that need to be kept in mind while selecting the right option for your scenario are:
1) Its main users are on mobile.
2) comments can only be made to parent question.
So I would suggest you to select option2.
The main and only action user can perform on this page is to comment.
In option1, the comment box is not in accessible area of mobile phone. There are 3 types of areas on mobile devices viz, Easy, Reach, Hard. The main actions that are expected from users are to be kept in easy area.Hence option1 is not a good idea.
Check image for reference
In option 3, the user will get confused in between 2 reply buttons making the screen less user-friendly. Also, it would be very confusing to decide that how the comment box would show up or animate on click of the top reply button.
So option 2 is perfect in your case. Additionally if you add functionality for comments on comments, you can add some left spacing before those comments, reduce their font size and you can keep the distance between 2 main comments more than two comments on comments.