The tension in the slide topper can be adjusted and that should help with the flapping in the wind. However if the wind is strong enough anything will flap. In most cases it sounds worse than it is.
If I were you I would put the topper over the kitchen slide for the very same reason you gave. There could be a clearance problem though as the awning roller would be in pretty much the same location on the trailer side as the topper. In my case the awning stops just before the dinette slide so I don't have the problem you have, but I nearly did with the RV I was looking to buy before the one I now have - it too had an awning-over-slide arrangement.