I'll come back to their objectives later but what has or will be 'realigned' that would constitute a success for City, let alone a major success? Beyond the wording of a relatively minor point, something that quite possibly will be redrafted to meet competition law, the only tangible change that we're likely to see is the change to an element of a rule that City voted in favour of and something that will have little to no consequence for any club. I appreciate you're a City fan but in what world is could that be seen as a victory for City?
Regarding your point about the Premier League. Firstly it's important to remember that the clubs are the League. Sometimes we talk about the PL as if it's some sort of independent body separate from the clubs when in reality Richard Masters is nothing more than an employee of the clubs. The clubs set the rules for their competition, which are often a massive compromise in an attempt to suit everybody (or at least 14 clubs), leaving Masters and co with a near impossible task of formalising what the clubs want. As I saw a sports lawyer quoted on the BBC saying, it will be an embarrassment for the PL however I don't think the clubs will care. We've seen similar procedural errors from the League in respect to PSR cases against Everton but just like in this case, ultimately the League won the argument so the clubs won't mind. They'll make some minor changes and the rules will be, give or take, the same as before.
City launched this case because of the 130 charges they face. They wanted to muddy the waters and undermine the PL as much as they could, even resorting to arguing against rules they voted for. We're talking about this case because it's been out in the public but City have been launching legal challenges to the PL's charges against them from day one (and like this, losing them). They'll crow about their minor victory (and ignore the fact that the vast majority of their case was dismissed) when in reality they'll be no better for it but they undermined the League and that was their objective.
You mention that the entire thing is a mess from the Premier League - I accept it's a mess but it's not just a Premier League thing. Football has been a lawless industry for too long and we're seeing the challenges Leagues are now facing in trying to implement proper rules and regulations. Again it's not just the PL - look at the mess with Barca where La Liga have implemented their rules. I'm not legal expert and have no idea how successful the PL will be with their 130 charges against City but one thing is for certain, the worst thing that can happen to football is if the PL don't win that. Even as a City fan, whether you'd admit it or not, you know full well that City have broken the rules (whether you agree with the rules is another matter) on a mass scale and if they were to be cleared, particularly with all the public evidence against them (you've seen the emails I'm sure), what would be the point of having any rules?