Would like to state that I tottally agree with OP.
This feature (that the fence rolls out on top of existing windows) I miss frequently.
It is very annoying to have to minimise all the open windows in order to get access to the icons in the fence. This also is true for fence that are so large you have to cross a window laying over the open fence in order to reach the icon on the bottom. When you cross the window your fence poofes away.
It was sooooo logical to have it implemented that an user at least does have the option to choose whether he wants his rolled out fences on top of all other windows because you know it is the choice and the wish of the user that wants access to the icons within the fence he unrolls at that moment. But hey, it is not too late, do it now and we be more happy users. Thank you