Whatever imbalance or mechanical problem caused the damage to the medial surfaces is probably the same thing that is causing the chewing up the backside of the kneecap. Two birds with one stone if you can narrow it down!
You're right, Knott. The post-op pt that has been prescribed in times past always addressed chodromalacia with strengthening exercises for both the quads and hamstrings and gradually increasing the flexion of the affected knee. When I wasn't due for spring cleaning of the knee, seems like I've had to meet with the ortho during the high point of my cycling season for pain around the kneecap, stiffness, and occasional swelling.

What it sounds like is a force production problem, a technique issue where you are doing too little hip extension to turn the cranks and therefore using too much knee extension.
Cyclingphysio, I've wondered if I haven't been using enough of my gluts. I have a tendency of raising my seat post a little higher--but not to the point that I'm rocking in the saddle. Maybe that causes me to use more of my quads than gluts? I had my saddle a little higher when I was using SPDs but now that I've switched to platforms, I've lowered my saddle about 3-5mm and I am able to keep my heel down as I pedal.