The AFL has tried to create a league where all the teams have an equal chance of winning a premiership, with a few exceptions. One of those exceptions is Sydney. They've removed the COLA (though they still benefit from existing signings under it), but Sydney still gets a big boost from their academy.
I tend to side with the AFL here. There is a net benefit to the AFL growing the game in NSW, and getting talented NSW kids playing footy instead of rugby is on balance a good thing. That works best if Sydney can reap the benefits, but it does mean they are more likely to be consistently good than most other clubs. They also know the AFL will bail them out if need be. Sure, the AFL was unhappy with Franklin's contract, and initially said it would count against the cap even if Buddy wasn't playing, but if they were struggling don't think for a second the AFL wouldn't relax that stance.
They escape scrutiny because they are a well-run club that gets more swings at elite talent than other clubs, meaning they can get a few things wrong and still be a good team.