Hi Gustav,
I think that is a very interesting idea, and it could work quite well if made in the way you described. I would first build the packraft and then make the rod holder afterwards, both so you can decide exactly where you want it, and also because after making the packraft you will have a very good understanding of what is possible and what will be too difficult to make. I think the most challenging part will be designing the attachment between the rod holder and the outside of the tube, but perhaps it will be easier if it is made as a straight slot instead of a round hole. To ensure it will work properly and remain airtight, definitely experiment with scrap fabric before you attach your prototype to the packraft. Cheers!