Remedy of this knee issue is absolutely the goal here, but I dont know if rehab is the right wording anymore given the suspected Patella tendinitis was not to be inline with actual findings.
The fact my knee connoisseur consultant could not find any issue structurally, alignment wise or any signs of previous healing and damage now means I do not know what I am trying to treat.
My current misguided plan seems to be to just get bigger & stronger legs in every aspect and see if that helps 
Trying flat pedals to work out a foot position is a great suggestion!
I’ve had knee pain like that that came from slightly twisted cleats. It developed halfway during a short local XC race - obviously I ignored it to finish the race, and then forgot about it. Did a few road rides and only had slight pain, but then a couple of days later I used the same shoes and got the pain back just 10 minutes into my ride. I remembered that I had recently changed cleats on both pairs of shoes, so stopped and adjusted the cleat, and the pain went away almost instantely. It wasn’t out by much, maybe 2 degrees, so it looked like it was sitting in the same place. Adjusted the other shoes too, and no more pain.
I would argue that it is. As long as there’s some sort of pain you’re trying to get rid of that’s preventing you from performing normally - goal is Rehab / PT as opposed to general strength building, power, hypertrophy, etc.
Not finding an explicit issue usually means it’s some sort of muscle imbalance or weakness. Rehab / PT focus until the pain is gone, movement is good, then maybe switch structure (if you want) to strength build, or even just stay maintenance / mobility.
I’ll say that was part of my “journey.” Misdiagnosed myself with quadricep tendonitis and tried treating that only to have it corrected by my primary as just patellafemoral i.e. bad knee cap tracking which over time can lead to Chondromalacia which requires actually getting a camera behind your patella to diagnose because it makes your patella cartilage look like crab meat. So in short there’s a confluence of a lot of possible issues in that area that can be tough to pin point so I don’t necessarily blame a doctor for not being super sure of what’s going on.
By my way of thinking I feel like for rehab purposes body weight leg stuff done at home is just as good if not better than gym work. Less, but not no possibility, of causing more damage provided you’re keeping everything in proper form and alignment during the exercises. Plus, you can just fit it into your day rather than having to find time to go somewhere to work on it. Stuff like step ups, step downs, pistol squats (only to a chair or stool, not the whole way down butt to heel) and some resistance band work (among many other options) can work wonders for strengthening the stabilizing muscles cycling neglects at a more gradual pace to help get your knee literally back on track. You might try Macconnell taping of the offending knee cap to see if that provides any relief. That would imply a case of patellafemoral. If it doesn’t help at all you can scratch that off the potential issue list and you’re only out a few quid for fancy tape(don’t expect a revelatory experience but if you’re thinking hey that’s an improvement it might be a thing). I don’t feel like doing any actual weight bearing/gym work exercise will sort this any faster and as has been said could cause more harm than it fixes.
Once your knee or knees are on the mend and it seems they’ve turned a corner would it be useful to actually work on pure strength. But honestly I don’t feel like I’m missing anything by not going to the gym to do heavy stuff. I only bought a kettle bell in the first place to do the fancy tests to my Favero pedals (turns out I was the problem) and just started incorporating it into my strength routine and it’s only 8kg. I now have a 10kg because progress. I’m doing this stuff to have a more complete approach to my fitness rather than put on a buncha muscle mass which adds weight which is why we spend extra money on fancy bikes to have less of. Through consistency and increase of reps have I become a tad more “swoll”? Sure, but it’s the functional muscle I’m looking for not really the big or “impressive” stuff. Just happens doing more than nothing has beneficial effect.
I haven’t bought them yet because my routine seems decent but there’s a couple books I’ve been interested in on amazon titled “Cycling anatomy” by Shannon Sovndal and “Bodyweight Strength anatomy” by Bret Contreras that are full of exercises and how to do them properly that could prove useful.
Thanks for the advice guys
Cringed so hard when reading about the idea of a camera behind the patella lol 
Will have further discussions with my fitter/physio and see what a proper in-depth assessment points towards.
Afterward, your doctor may request any of the following tests to aid in diagnosis and grading:
X-rays to show bone damage or signs of misalignment or arthritis
magnetic resonance imaging (MRI) to view cartilage wear and tear
arthroscopic exam, a minimally invasive procedure to visualize the inside of the knee that involves inserting an endoscope and camera into the knee joint
Just grabbed that off healthline.com through a google search of chondromalacia just to make sure I wasn’t misremembering. Does imply that your MRI could/should have shown something so I definitely could be off there. Feel like we need to start these threads with the “doesn’t constitute medical advice” disclaimers that are common amongst these kinds of talks. Or at least the fantastic American pharmaceutical advertising phrase “ask your doctor if any of the BS you just read is right for you.”
Update on this, incase it helps anyone else.
Went for a second opinion from another consultant. He was far more in depth and whilst agreeing with the initial consultant that there was no major issue, there was three pertinent issues which could certainly not be helping the situation.
So three mechanical disadvantages, but nothing he would recommend surgery for unless they get seriously worse.
Fortunately though he was happy to write a recommendation for my insurer that I be referred to my specialist bike fitter/physio rather than just the guy at work & a biomechanist at the same time.
Hopefully some of the above can be resolved through physio work. Probably only #2?
You may not be able to treat those three specifically, but still sounds Bike Fit, and Rehab / Physio work evolving into a permanent strength program will help.
It would be worth your time to see an injection specialist for evaluation of a corticosteroid into Hoffa’s fat pad. Bring down the inflammation and then hit with PT.
Knees just hurt sometimes, is inadequate when you have a specific mechanism of injury and reproducible pain patterns. MRI limitations mean soft tissue injuries and biomechanical issues don’t always show up.
I’d seek a second opinion from a sports medicine physician who specializes in cycling biomechanics, not general ortho. I do my medical checkups through Dr. Tina Sindwani’s concierge practice in NYC and when I had multiple specialists giving me dead ends, she coordinated referrals to better specialists quickly instead of waiting months between appointments.