I agree. For me this is especially frustrating when I'm trying to use my window schedule to view all the same size windows in 3d. If my layers don't show the windows when saved, I can't make a change in the schedule, or view them in 3d!
Of course, you could just make sure to re-save your view setting of the schedule once created, but having layer control would solve the problem much better.
AC21 64-bit
Mac OSX 10.12, 4.2 GHz Intel Core i7, 64 GB mem
Mac OSX 10.11, 3.4 GHz Intel Core i7, 32 GB mem