The PER model is like any other statistical model - it's been "fitted" to describe the data. It describes some slices of the data better than others.
Now with PER there's a further complication which is that it's user-defined. Hollinger picked the parameters himself, and necessarily so because there is no objective summary measure of player quality (hence demand for something like PER).
Given that it's user-defined, Hollinger surely "fit the model" so that it would pass a sanity test. My guess is that he understood that for most people the sanity test would involve comparing the PER-based top 20 list to their own list. It might also involve comparing the PER-based list of "unappreciated gems" to their own internal lists (hello, Manu Ginobili). So, Hollinger almost certainly tweaked his parameters to dovetail with those external pressures.
What this means is that PER was built to give a pretty good ranking of "typical" star and starter-type players, who all play a lot of minutes. It's also somewhat useful for identifying valuable bench players (though no more so than per-36 stats).
Now, like any model it's not going to be very good at describing or ranking "outliers," and both Wright and Rondo are just that. Point guards who rebound like power forwards, or who shoot 60% from the line just are not going to be well-captured by something like PER, because the model wasn't built to describe/compare players like that. It was built to compare Nowitzki to Wade, and 2008 Lebron to 1988 Jordan.
Similarly, guys who shoot 74% from the floor and have terrific per-minute block numbers, but who also can't get more than 18mpg, are outliers.
No summary model is going to accurately capture guys like Rondo and Wright, because they just lack "comps" which is what any informative statistical comparison requires.
So in sum: PER is flawed, but not much more so than any other summary measure of things that are complicated. And I think if you recognize what Hollinger probably intended it to do - which is provide "sensible" top-50 lists and comparisons of great seasons across players - its anomalies become more understandable.
And to answer the OP, comparing Rondo and Wright based on PER or any summary measure just misses the point because they're so unique. It's like using one of those summary "city quality of life" indexes to compare New York and Boulder.