One thing I do seem to notice when comparing a young budding big man's production is that they are usually more efficient than a young swingman
I think the reason for that is that big men tend to be more efficient (talent for talent), not that PER unfairly skews to big men. PER isn't flawless, but does a fairly good job of putting numbers like scoring, rebounding and assists in context for pace, opportunities and efficiency (i.e. scoring 20 points is valuable when done at a certain efficiency and really not valuable if done using lots of shots/possessions). That's the reason why talented big men are so sought after...they tend to score more efficiently (since they play closer to the hoop by and large), they tend to rebound a lot more for the same reason and due to their inside-out role in the offense, they tend to help their teammates score (and get assists for that) but don't turn the ball over so much since they do their helping teammates without dribbling a lot.
Now, all of that doesn't apply to Oden (notably, the fewer turnovers) but they are all reasons, I think, why (talented) big men tend to show better in PER. They simply are more efficient, at comparable levels of talent.
but I do have a problem with your take on Durant's defensive potential.
I didn't render a take on his defensive potential.

I just said that his strength was more the "box score" stuff, while Oden's strength so far has been non-statistically tabulated defense. I think that's quite accurate...Durant's no defensive stopper and Oden has generally been a defensive impact-maker (when on the floor, of course...staying on the floor is a problem for him, no question).
I don't really have an opinion on Durant's defensive potential. The tools are there for him to be a high-level defender, but the instincts and technique aren't. Those generally boil down to motivation and endurance (lots of players would like to work hard on defense, but have trouble doing so game after game, especially when they carry much of the offensive burden). Will Durant have the motivation and stamina? I think that's pretty much impossible to know. I hope he does. I love watching good/great all-around perimeter players.
I'd venture to say his hot streaks are going to be more valuable than Oden's 'defensive flashes of brilliance'.
Well, I'd say it's more than flashes. I think Oden is great defensively 90% of the time he's on the floor. His "flashes of brilliance" come on the offensive end. I don't know if Oden will become consistent on the offensive end, but I think he will with experience. I think those "flashes" on offense show that he has the capability to become an offensive force. But, again, it'll require staying on the floor...to give him more experience and to get into a rhythm in games, rather than making constant trips back and forth to the bench because of fouls.
To be clear, I think Durant is a fantastic talent. I think he'll be a top-five perimeter player in the league during his prime. He's as natural a scorer as Kobe, McGrady, Carmelo, LeBron and Wade. The main questions are will he become a play-maker for others and will he become a solid defender? If he doesn't, he can still be Carmelo Anthony, which is pretty high value. If he does, he can be as good as Kobe or McGrady before his injuries. (Hard to imagine him becoming as good as James, but in my lifetime only Jordan was at or above James' level.)
Of course, I think Oden is also a fantastic talent. He's already an elite rebounder and a high-level defender (with only his foul rate, really, holding him back from elite defense). He has the the tools for a very good offensive game and has already shown the development of it. I think that within a couple of years he'll be on Dwight Howard's level and has the potential to surpass Howard. Assuming that that offensive development continues. That and health are his questions.