As bArt2 described you get the blinking box instead of the pop up feature. The same is true if you leave the secondary indication on the lower DU instead of blanking it.
I do agree though, the upper DU becomes a tad cluttered if you have compacted secondary engine indication up, status messages for datalink and ACARS and some autoland message. However it is a way to keep those indications in scan while watching the girls on the lower DU.