I, for one, would love to have this feature.
I do a lot of student workbooks where the same document is used to print the Student and the Teacher's versions. Both versions are essentially the same with the difference in the footer and the fact that the Teacher's version has a 5th color plate for the answer key.
Now If I could put my footers on a different layer than if would just be a matter of activating the proper layer depending on the job I wish to print.
Other situations involve having master elements "floating" above other page element. This cannot be currently done as any Master element is set to be on the background layer. This involve a lot of time wasting "Bring to Front/Send to Back" shuffle.