One big difference between the KLR and the KTM is the choice of luggage. On the KLR, I decided that would keep everything in line with my body. After all, my body is a large, high drag body that just about doubles the frontal area of the bike. So, I chose a trunk and a large tank bag.
Of course, one of the downsides of this approach is that I had to "step thru" which isn't easy on a tall bike. The other potential downside was that the side view cross section area was large and high which might cause problems in a cross wind. Cross wind stability has been a consistent problem on the KLR. I remember getting off the highway and parking on a side road facing into the wind because I was afraid I was going to blow over if I kept riding.
On the KTM, I bowed to being a bit older. I knew that at some point "stepping thru" was going to require flexibility I wouldn't have. So I went for a small tank bag and panniers mounted as low and forward as possible.
I also hoped that the KTM would be better in a cross wind, but that didn't work out so well. Of course, the KLR wasn't perfect in a cross wind, but I would have to say the KTM is worse.
Imagine you are riding on a highway, 10 mph below the speed limit and leaning into the wind 10 to 15 degrees. It feels like the tires might slip out from under you and when a gust comes along, the bike is moved over by 1 lane or more. Scary stuff.
However, there is a technique that is helpful. The scariest part is the bike being moved sideways, especially if that puts you off the road. It turns out that, if you lean way forward, you put more weight on the front wheel and move the lateral center of pressure forward. In this position, the bike doesn't steer away from the wind as badly. You might even balance out the front and rear so that you are still leaning, but the bike doesn't feel like it's going to slide out from under you.
In the end, the choice between trunk and panniers isn't really a side wind stability thing. Tall bikes are bad for side wind stability either way. At least with the KTM, I can lean further forward as I am not limited by the tank bag.
