I agree with this regarding the position going forward. I think the amendments required to the rules to make them compliant are relatively straightforward and not particularly dramatic (although possibly still a win in City's eyes). Of course, the PL will also have to pass a vote with new drafting in and that may not be straightforward depending on how the various interest groups among the PL clubs shake out.
The historic position is however much more complicated. The problem is that without the inclusion of shareholder loans as APTs, the rules are unlawful. And it seems likely that several clubs may have failed PSR if they had been included (or even if not failed, had less headroom and been able to spend less). You might say that if they'd known this those clubs would've restructured their shareholder loans. Maybe- probably, even - but it's not certain.
So this means you have a situation where some clubs have been punished under unlawful rules when their competitors (who may have breached equally or even more severely if the rules had been lawful). I do see that as a really difficult problem for the PL to resolve.