I'm getting the sense that this to a very real degree comes down to that old "Only if you run it that way" argument.
Which isn't a problem, it's just that it also falls into "I just disagree" territory.
I think it's not unwise - from a design perspective - to design a setting the way they did, accounting for a certain type of jerkish behavior some players are known for rather than making one particularly vulnerable to it.
It is, afterall, a lot easier to redesign lower level versions of NPC's than it is to tack on a whole bunch of levels.
Pretty much this.
For me, it comes down to GMing 101: You can change things. The stuff in the books is the baseline view for the setting, set that way for all the reasons people have delineated above (PCs are bastards, NPCs raiding places, etc etc.)
You can certainly alter anything you choose to flavor the game for yourself and your players. There are good reasons to have lower level rulers, or higher level, as long as you are capable of addressing the questions that come up from your players. Heck, the designers are great but don't always take everything that PCs can think up into account and you have to add protections from things they'd never think of. This has become more apparent in recent years in things like comics, where they've had to address why supers haven't killed the President or taken all the nukes and so on.
As with everything, they've given you the beginning of the game but if you have specifics in mind you have to adjust what is written to take that into account.
tl;dr: The trope exists as a baseline.