The whole "exchanging fat for muscle" thing is wildly exaggerated. It really doesn't happen to any significant extent. You'll put a little muscle on your legs from cycling but at most probably a pound or two. When people claim they stayed the same weight but gained muscle, it's mostly wishful thinking. It's hard to put on significant muscle even when exercising specifically for that goal and intentionally gaining weight. It just doesn't happen accidentally from cycling to work.