[patosai]

I've never worked on stealth aircraft, but energy has to travel from the transmitter, through the aircraft's radar cover, off the array itself, then get back through the cover and back to the receiver.

There are probably ways to filter for specific RF frequencies on the cover so only those in specific bands can get through, then the array itself might absorb some portion of the energy that gets through. The array also might be at an angle so waves are reflected in a different direction, or there might be radar absorbing material placed in specific spots that helps minimize reflections. I think the arrangement of elements in the phased array itself could also lead to reduced RCS at certain angles. Again these are just educated guesses, I would imagine the details are classified.