'Mild chondromalacia' in right knee

Before describing my problem, some background information:
21 years old male
173lb bodyweight
Years of lifting weights: 4
Years of taking lifting heavy weights and taking powerlifting seriously: 2
History of serious injuries: none
History of knee discomfort while lifting: none

Description:
It all started one day in December last year when I went to the gym and to do some bench and squat. I remember doing 3 sets of 8 @ 9 with 225lb and it felt really really hard, something unnusual. After that, a friend and I had to run to catch the train and also go up some stairs and I remember my right medial vastus being really sore and ‘stiff’. The day after I felt some sharp pain in the medial side of my patella when walking, I didnt mind it and luckily that day didnt had to train legs. Two days after I didnt have any pain and then continued my program (which was an awful program) and did 3 sets of squats getting a reps PR at the last set. Some days after I started to get mild pain while walking just below and in the medial side of the patella. I stopped heavy lifting on the squat and deadlift for two weeks and that discomfort disappeared. In Januar, I got a new PR in the squat and I was feeling great, at the end of Januar I started getting the same pain as before and decided to rest again, this time I was feeling some discomfort and I didnt feel completely healed. I was training with fairly low intesities and was feeling the above described pain the in the knee and decided to visit the Ortho in March. He told me I had patella tendinitis, gave me a bandage and told me to rest for 4-6 weeks. I kept training but doing some tempo squats with 135lb and some isometric squats as well. I started to feel better and started to lift some higher intesities in the squat and then started to feel some discomfort in the knee. This time it felt like some sort of pressure bellow the patella tendon while walking. I didnt feel nothing while going up the stairs or even doing light squats or jumping. I went to the same Ortho and he prescribed me an MRI. The diagnosis of the MRI was mild chondromalacia, my Ortho said there was nothing wrong with the knee joint and acknowledged the mild chondromalacia. I asked if I could keep training and he said yes but very light and progressive.

Current situation:
I feel discomfort while walking right bellow the patella tendon and in the medial side of it. Some days I feel it more than others. This is how Im training on leg days:
Leg press , 3 sets of 10 @ 7 → no pain then doing these / Tempo squats 303 with 155lb → no pain (in some reps I would feel some discomfort, but does not prevent me to complete the set)
Sumo deaflift 2 sets of 5 @ 7 → no pain doing these Hip thrusts 3 sets of 12 @ 8 → no pain
Ham curls 3 sets of 10
Calf raises 3 sets of 12
After doing these exercises and having my legs warn and worked out me knee feels better. Days after I could feel the above described discomfort, some days I could feel it lighter, some days I could feel like if my knee was healed. I am doing this for about 3 weeks already.

Questions:
Is what Im doing currently good ? If I continue feeling pain/discomfort, should I visit the same Ortho again?
I was thinking in getting the hypertrophy gpp template for now, would it be ok to run it?
What are the red flags for this condition?

Something to add:
I visited a PT who checks lifters. He said my quads, hams and calves were tight. He told me to strenghten my posterior chain muscles and to do some stretching for the quads. He said that my knee pain is most probably caused because of bad form doing squats. Well I was stretching my quads but I didnt feel anything better now.

PS: English is not my native language, so if some clarification is needed please let me know

Yes, I think you’re on the right track and should be treating this like a patellar tendinopathy. (This may help: https://www.strongerbyscience.com/squatting-with-patellar-tendinopathy/ )

No, I don’t think you would need to see the Ortho, because the “mild chondromalacia” seen on MRI is irrelevant, and based on the findings you don’t need knee surgery.

There are no real “red flags” to be worried about here, and discussing catastrophic knee injuries is just likely to make you more fearful.

Re: your PT findings -

I’m not sure how it’s possible for someone’s quads AND hamstrings to both be “tight”. In fact, there’s no consensus on what “tight” muscles mean anyway, and I don’t think stretching is going to help you.

It may be worth a form check on your squats, and maybe using some knee sleeves.