Cracked and sagging floor

There is at least one example/thread with picture here of floor cracking at the perimeter of the factories reinforcement plate(s). So the plate didn't totally prevent sheet metal cracking.
Body plugs are typically installed from top down. I dont know that it makes any difference one way or the other. Could you step on the raised side hard enough to push it out? Maybe. That hasn't happened yet. Go ahead and flip them since you have the carpet out.