Odyssey simply continues the trend that most players will follow the path of least resistance, as opposed to path of best results. Back when the Engineers were introduced, one fairly common bit advice was to look for anarchy systems to get manufactured materials, because murder there was "legal." Of course, there's
plenty of wanted ships in non-Anarchy systems that you can destroy without consequence, even wanted transport ships, but that would require paying attention to what you're doing, scanning ships, and potentially getting into a fight with a non-optimized ship if you do this while also running missions.
As for the Superpowers turning a blind eye to the Pilots' Federation's ongoing criminal activities... It's part of the lore that the Superpowers, as well as minor factions, all rely on the Pilots' Federation to not only administer the bounty system, but do their dirty work. And it's
now part of the lore that the Pilots' Federation is collectively manipulating even the Superpowers for power, profit, and fun.
The world of Elite, draws heavily from the Cyberpunk genre. From corporations being
actual governments, through government conspiracies, to criminal cartels dominating the locals, the world of Elite Dangerous is not too dissimilar to the dystopian future of that genre. Heck, slavery is fairly prevalent throughout human space: many independent governments permit chattel slavery, there's the heavily regulated indentured servitude in the Empire, and corporate governments practice form of slavery called peonage.
In most Cyberpunk settings, there's always one corporation that is the setting's "Big Bad." The one that is behind what the plucky anti-heroes are investigating. I find it amusing that when you look at how Frontier has designed Elite Dangerous, you can easily come to the conclusion that over the centuries, the Pilots Federation has morphed from a trade union of transport pilots, to being the force behind everything that's wrong with human civilization in the 34th century. Collectively, we're the third most powerful Superpower in Human space (sorry Alliance), and we use that power for fun and profit, even at the expense of ordinary citizens.
Let's face it: we're the baddies.
Source: https://www.youtube.com/watch?v=8JOpPNra4bw