I've never built a pocket rocket stove, but I can see its appeal thanks to the simplicity of design and construction. If the setup that you propose will work to warm up water efficiently, I do not know, that is something you will have to build and make some experimentation. Of course if you do not post pictures/videos of this construction and stove use, it never happened...
You have to take into consideration that water has a high thermal mass and it will absorb a lot of heat from the pocket rocket stove combustion chamber, rendering combustion less efficient, you will have to use more wood to reach the same temperature and it will produce more smoke.
I suggest you make the pocket rocket stove as a first trial to learn how to warm up water with wood stoves and as you get more experienced on the issue you can try other stove designs.