I have a kayak trailer for my bike, and have done some touring with bike-kayak combo as well.
My bike is a 700c hybrid, with no couplers, and there's no way I could carry it in a closed top kayak. Additionally, the trailer (
http://www.tonystrailers.com) does not collapse easily. So I can freely choose where I want to paddle, but my paddle routes will have to be from point A to A (where my bike and trailer wait).
A kayak (or a canoe) is rigid enough not to require a massive trailer. If you look at Renata Chulmska's pic, you see there's just a pair of wheels under the kayak, and a towarm attached to the bow. The problem with closed top kayak and this arrangement is that you need to come up with some kind of attaching system in the bow. This more than likely requires some modifications to the bow. I was not too enthusiastic about modding my kayak, so my trailer is basically a flatbed. When loaded it does utilize the kayak's hull as a part of the structure, making the trailer itself more simple and lightweight.
I'd agree that Renata probably did not carry her bike in the kayak either. You
could try that with a 2 seat kayak and a folder bike, putting the bike in front paddler's seat. I seem to remember someone has done this, but could not find a link for now. You would also have to balance the load in such kayak very carefully, otherwise there's no way you can keep it going against any kind of wind. And you would still have to come up with the towarm attachment.
Open-top canoe and a folder would be less hassle. Towarm attachment would be easy (there are several commercial solutions for this, or you could rig your own) and loading the bike in canoe, properly balanced, would be easier. You would lose some seaworthyness with this combo, though. That may or may not be an issue in your case. In my case it was the deal breaker.
--J