Julian coached Donovan and the "structure" of how NOP was run was pretty clear right? Salazar had a "select" group - the superstars or how should I put this, the ones who were clearly willing to do whatever, ahem, it took to stand on the podium at the Olympics and Julian had the "best of the rest" which included Brazier at the time (because he had missed Rio and wasn't yet the world champion Donovan Brazier that we eventually saw).
Regarding your earlier point about it being possible Brazier just did what he wanted - possibly against the advice of Julian and "what should Pete have done, let him go?", and this being behind his potentially career ending injuries, I guess it's plausible but at least for me, not overly likely.
I think in your average athlete/coach relationship thats more likely to go down (ie. lets say a coach that sets a plan, the athlete acts on 75% of the time on their own and thus it being hard for the coach to monitor exactly what his/her athlete is really doing), but in these highly-funded pro setups where training was like going into an office every day, it's hard to imagine PJ didn't or couldn't see what was going on straight away. At least for me, the issue was not the first injury - that happens, but it's how botched and mismanaged the recovery was. He was first hurt in that 600m in Hungary in 2020, yet then ran on it days later in Stockholm in a total meaningless season. They then had him run an indoor race only for it to be an issue after that and it was just 1 step forwards, 2 backwards all of 2021.
You are right, Brazier was a pro athlete - but still a kid. At this age and with his talent I think many posters on this message board could have written him a program and if he was healthy, he would have run incredibly well, but it's in the moments of adversity and uncertainty where the true value of a competent coach comes in. Making sure there isn't panic to run "just more race" or "test my form in this race". The injury post 600m wasn't so critical he couldn't run (he ran sub 1.44 in Stockholm just after it) so again in my opinion at this point there is no reason it wasn't fully recoverable from. As it was it just got worse and a stress fracture that turns into a full on break is an overuse/over-stress thing. That's coaching. The same thing happened with Klosterhalfen who suddenly regained form and started to be get healthy again as she was transitioning away from Julian towards the end of the 22 season.
There is just too much evidence at play to not draw some logical conclusions I'm afraid.