If it means anything, my son's 2001 Civic does the same thing, and I originally took his car into the dealer regarding the strange click/clunk from reverse to drive, but was told too it was the calipers shifting.
So when this problem started on my MDX, I just knew it was a Honda *thing*. I know some people don't like to accept it, but for me, as long as my car is still safe to drive, I'm cool.