I am not too happy with message boxes appearing on the MDs as well.
But you really should include your TV into the LMCE picture. It is SO nice, to have LMCE take care of turning on, tuning in, and adjusting the TV set to each program, and adjusting the receiver based upon listening to music, or watching a DVD. That's what LMCE is about. To have control over the environment, without the need for other remotes etc.
Regarding message boxes: There is an option to only show some messages on an Orbiter. You might want to play with that.