I am not getting the distinction you are making between her explanation (as I understood it) and yours. Hers: squats weren't activating an area of my quad, leading to underdevelopment. Yours: squats aren't activating an area of my quad [due to arthrogenic muscle inhibition, a central nervous system mediated process], leading to underdevelopment. I.e., I don't understand how you can say you are suggesting a completely different mechanism when she didn't offer a mechanism. She just observed my quad underdevelopment, accepted that I had been squatting, and concluded squats weren't activating it.
Are inferring from her recommendation of isometrics that a particular mechanism is at work that is different from your mechanism? E.g., "The PT believes that there's a lack of activation due to issues with local innervation, as shown by the exercises she recommends, whereas actually the problem is a central nervous system problem, which the exercises she recommends will not fix"?
Last time I was lifting heavy consistently, which was up until late September of last year, I was trying for one heavy deadlift set of 5, then one backoff set of 5 about 10% less. It was becoming very hard to progress sets of 5, so it would often turn into, say, heavy sets of 3 and 2, then a backoff set.
On squats I was alternating between a day of 3X3, then a backoff set of 10 at about 2/3's the weight (e.g. 3x3 @ 350, 1x10 at 225), and sets of 5 across. Squatting and deadlifting on alternate days: deadlift/bench, squat/press. Training about 2x/week, doing some chins and curls on off days.
Age 52, 6'6", BW about 275 at the time.
The difference is that your understanding of what she said is markedly different than what she actually meant. You, by virtue of being a reasonable human being who is obviously quite intelligent, reasoned better than your medical provider did.
It is commonplace in the PT community for PTs to identify specific weakness of lack of activation in the VMO, and that is not supported by the evidence to any degree, that I have seen, and their prescription for it is to do targeted isometric exercises to directly stimulate the VMO.
My proposed hypothesis is actually what you believed she said, even though she did not mean it that way. Your entire quadriceps, not just the VMO, is not underdeveloped but, rather, has had a centrally mediated inhibition where you aren’t able to activate it. The muscle is there, but the brain is not using it effectively, and the lack of motor recruitment makes it loom smaller. This is seen almost immediately in someone with a massive meniscus tear or ACL tear. Within hours, their involved quad looks markedly smaller than the uninvolved side. I hear PTs, all the time, say things like, “Quad weakness led to the ACL injury” and use the presence of this phenomenon to justify this hypothesis.
Until you do something about the intra-articular pathology that is causing transient effusion, you will not be able to remedy this. There are good ways to rehab a torn meniscus and straight leg raises are not it. Her hypothesis has led her to conclude that a man who weighs 275 at 6’6” and was squatting 350 at over 50 years old has weakness that is going to be addressed by isometric exercises. If you were 6’6” and 675#, I might suggest that this is a decent and reasonable prescription given the fact that your overall activity is probably so low that this amount of exercise stimulus is likely to give you some adaptive inducing stress. In your case, you’d have to take these straight leg raises to multiple sets of absolute failure, have someone do forced reps with you, and even then, you are still only moving the knee to a singular joint position. Meniscal pathologies require large, controlled ROM, as well as external load.
Your training history is going to require that you rehab like someone who is strong. You are also going to have to still induce enough stress to force the CNS to be forced to engage more of the muscle, and that will also require that the exercise prescription and symptomatic treatment addresses the recurring effusion.
And before you ask, no, I’m not saying to just bang your head up against the wall doing the program. An experienced coach can take one look at what you were doing and give you something better.