Chondromalacia patella is an abnormal softening of the cartilage of the patella. However it fits within a larger group problems with the knee cap and is known as patello-femoral syndrome. Chondromalacia patella is an older term and was used in rather a blanket fashion. So even now it sometimes gets overused when you just have signs of patellofemoral syndrome. However you can have all the symptoms with patellofemoral syndrome and not have chondromalacia patella. The physio for either condition is much the same but it may take longer with chondormalacia patella due to the changes in cartilage.
Chondromalacia patella should be diagnosed from loss of cartilage seen on xrays or CT and you need to have a specific sort of xray called a "sunrise view" which it sounds like you have had. Not just based on cracking noises when you passive glide the patella against the femoral bone
in Patellofemoral syndrome, including chondromalacia patella, you may have changes in the way the patella works in the joint such as
• it failing to track correctly in the joint when you move your knee joint with your quadriceps muscle
• small or misshaped patellae
• Increased Q angle
• Weakness of the part of the quariceps on the inner side (vastis medialis obliqus)
• tightening of the tissue ant the front of the join on the outer side (lateral patellar retinaculum)
• Tight/overactive hamstrings muscles.
It sounds to me the physio gave you rational exercise but your physio should also have checked out the above points. The issue with the increase in knee flexion angle while working the quadriceps the greater the force is placed on the joint. The purpose of the exercise is to increase the strength of the quadriceps muscle including and also cause the joint cartilage to remodel in a useful way that will make the joint and cartilage more functional and more healthy.
The exercise has to be balanced and incrementally increased so that on one hand you don't flare up the inflammatory process (most likely reason why you feel the pain and swelling later is stirring up the inflammatory process with the disorder) but on the other hand challenging enough to increase the strength of the muscle and to stimulate remodelling of the cartilage
Gradual increase in the angle while strengthening sounds a good idea. Using the reduction in pain and inflammation later as a marker for increasing the challenge of the exercise sounds good. However there are a few things to consider:
• Ice packs or anti inflammatory gel can help if you apply them immediately after the exercise. Menthol cream may help the pain but isn’t reallyanti-inflammatory
• Have the knee cap assessed for poor tracking and having the knee taped may sometimes help reduce the abnormal force on the joint while exercising and thereby reduce the pain and inflammation so you can do more. As long as you don’t have any skin problems with sports taping this may be a good point to discuss with your physio
• Closed chain exercises may actually be more effective than open chain exercises. “Closed chain” means the weight is going through the foot as with squats whereas open chain is where the weight is not going through the foot as in leg extension machine. Probably a variety is good but if you are having problems the closed chain variety may be better.
I don’t think there is any golden rule for restricting the joint range for exercising – you should base it on how you go. However you can hit a ceiling where you just can’t increase the range without aggravating the joint and you have tried this gradual increase including trying taping, closed chain exs etc. then you may just have to accept that you can’t do much more. However the remodelling doesn’t happen within a few weeks. You do have to persist for a long time.
Increase in popping on bending may or may not be significant. If it is painful then that is concerning. You may be “overtraining” If not it may be due to changes in the force across the joint and it may settle down more in time. If the cartilage hs really worn away then the cracking can be due to bone rubbing against bone but that sounds unlikely since your xray was good. I would be more guided by getting stronger, able to do more such as squats without causing pain and inflammation than by cracking noises.