I can't be sure it wouldn't have arisen, but it has indeed been confirmed to me more than once (kinesiologist, physiotherapist) that the shoes had been problematic because they led to wrong posture correction and that led to a transfer of energy (post absorption) to the wrong places. There is more than one way to that things could have been better, for example I could have strengthened my muscles on either side of the knee to hold it in place or I could have practiced the correct posture without shoes, but ultimately the shoes were both a major part of the problem and also the only thing that I, as a beginner, was able to focus on and do something about.. until it was a bit too late, and I was going to clinics to figure out why that pain was present. Which is kind of my point: as a beginner you're not knowing yourself or the field well enough to know better.
It seems like you're drawing a direct causal relationship to what is a very complex chain of events over a long period of time. How can you be sure the problems would not have arisen regardless of what tool (shoe) you originally bought?