I struggle to see how you have reached that conclusion. That's not suggesting you are wrong just that my thoughts are quite different. Both sides can of course claim a win, and for the PL they have had confirmation that the APT rules are sound in principle.
But whilst City took them to court to fell the tree, using your analogy, there were certain branches that weighed heavy and were the true target. And those branches have been cut. In doing so, the PL are left with a tree that might not survive.
Remember that the PL had legal advice on the rules, then amended them without (or ignoring) that advice. Certain rules voted through have been found to be unlawful. Those rules were ones that caused City to lose out on lucrative new sponsorship. It's going to take a hell of a lot more than some gentle pruning to get a lawful version of the rules voted through. The amendments were clearly made to appease clubs who saw them as enabling City to potentially grow revenue. Removal of certain words was paramount to getting them voted through. To think the PL simply re-draft and then get sign off is naive. They either manage that, and City are likely to then secure new sponsorships, or they again introduce a set of unlawful rules. The emails City have issued to all clubs suggests the latter isn't an option they have.
Stepping back, it is who you perceive to be the bad guy. The PL is essentially doing what it is under pressure to do. Certain clubs have clearly forced through these rules. The PL possibly doesn't have an issue with a lawful version, but many clubs will. Between them, they're in a spot of bother.