I've found that the peli cases are a little harder to fit comfortably into a kayak (at least the medium-sized ones). Having owned both I like them for different uses:
The peli case is great for crush protection and is quite durable/waterproof. If I'm bringing a camera mountain biking or throwing it in the back of a car I'll use my peli case. I tried cutting out some foam from the stern pillar of my Karnali that the peli case could slide into, but it was still pretty awkward to fit into the stern. Between the legs probably wouldn't be too comfortable due to the rigid nature of the case.
I use my Watershed whenever I go kayaking. It's bone dry, I've heard great stuff about the company, and it's very comfortable to slip between your legs. Get the padded insert for the bag and your camera will be safe.
Let me know if you have any other questions.
Fluid Glass Network