There are various parts of the 'layout' that are not copied when the /copylayout command is used. e.g. hotbar sizes chat windows (if the layout being copied has more chat windows/tabs these are not created). Also, filters are not copied so not only do you have to create new chat windows/tabs you also have to set all the filters. I'm sure there are other things that do not get copied.
A lot of settings are not copied as well such as "Use Tell Windows". I hate using tell windows, and every alt I make, I have to remember to go in and uncheck it.