Okay, I have a chance to actually look at the stats more closely:
1. Pettersson-Schultz has been pretty predictable this year IMO, a good offensive driver while being bad defensively. It seems like the pair hurts the team more defensively than he helps offensively in terms of relative stats, but the pure on ice results are still good
2. The stats for JJ-Marino also match the eye test, non-factors offensively but absolutely great defensively. Johnson has actually been a somewhat better offensive driver than Marino has this year (-6% threat level for JJ, -13% threat level for Marino). I think the 3rd pair has probably been better than the 2nd pair this year, but you're comparing 2 pairs with extremely different results.
3. Dumoulin has been their best defenseman this year, he's the only D on the roster who has been a net positive both offensively and defensively (Letang's a negative defensively relative to the rest of the team).
4. Crosby's line (so Guentzel and Simon as well) has really carried this team's good offensive numbers. Crosby's been terrific offensively (+34% threat level), while the rest of the team does nothing offensively (-7%). On the other hand, Crosby's line has been bad defensively this year, while the rest of the team has been great defensively. This is probably due to Malkin missing a lot of time, though.
5. Malkin's been great offensively this year, but god damn he's been a defensive train wreck. He's at a +4% threat level defensively while the team overall is at a -17%.
6. Bjugstad does nothing positive defensively while hurting them offensively. Hornqvist, Galchenyuk and Rust does nothing positive offensively while hurting them defensively (although a small sample size in Rust's case).
7. Lafferty gets crazy overrated on here based on his actual on ice results. He's a slight positive defensively while being a huge negative offensively. Blueger is in a similar position, although better defensively.
8. McCann, Kahun and ZAR have been asininely good defensively while Tanev isn't far behind them. Kahun has probably been their best analytical forward outside of Crosby this year.
9. I think Tanev deserves his own point here, he's similar to Lafferty in that he's a massive negative offensively, but he's also been a huge positive defensively and he draws a ton of penalties.
Overall, while the team results are good, I think this is a pretty flawed team. Not flawed as in "bad", but flawed as in specialized. Things aren't evenly distributed like you want to see, you have 2 offense only lines and 2 defense only lines. I think a 3rd line with Kahun and McCann as 2/3rds of it has been showing signs it can become a positive both offensively and defensively, but it's not quite there yet. Your 4th line is capable of being a legit shutdown line, but they'll provide next to nothing for you offensively. All of your offense is going to come from your top-6 if the 3rd line doesn't develop further. Your top-6 will be bad defensively, but that's fine as long as you have a great defensive bottom-6 (which they do). It's the same thing with the defense, the top pair is great, but the 2nd and 3rd pairs both have 1 huge strength and 1 huge flaw.