Well.. while one of my favourite things about the Duckverse is how it plays fast-and-loose with canon and has room for stories of all kinds... nope, PKNA cannot be canon to it. I tend to view most if not all Duck Avenger stories as taking place in an alternate universe, and PKNA just takes the "alternate universe" thing one step further.
I've already mentioned that I don't like the DoubleDuck stories, partly because Donald feels like "Donald in name only" (I did say that the stories read a lot like self-insert fanfiction.) When it comes to PKNA... I'm a lot more lenient. The Duck Avenger, particularly the one in the PKNA stories, is certainly notably different as a character as well -- but in this case he's a lot more acceptable as being a "mask" or a role that Donald plays. The Duck Avenger, for all intents and purposes, is an act -- but he's also a reflection of various parts of Donald's personality.
The interesting thing is that if we look at the Duck Avenger, such as he has developed over the years, which parts of Donald's personality he reflects has changed pretty drastically.
The earliest Duck Avenger is a pretty despicable person. He was created as an identity that Donald could adopt to get vengeance on everyone that had made his life difficult -- problem is that the Donald of those early Duck Avenger story almost deserves to have a difficult life. He's a mean, petty and jerkish bully with few-to-no redeeming qualities, who treats family and friends like garbage and then gets upset when they understandably don't want to give him the time of day. I mean, in that first Duck Avenger story he literally kicks a puppy. And so the Duck Avenger, as an "avenging" role towards Donald
This did thankfully get better in later stories. After the Duck Avenger more or less stumbled onto the idea of crimefighting, he slowly became more genuinely heroic, even if he tended to use dirty and underhanded methods and was mostly out for himself, but Donald got more of his positive qualities back so that you could root for him in those stories again and his victories felt earned and deserved. As years went by, the Avenger started playing less dirty and became more altruistic. He still had that edge of mischief about him, but became more affable.
If you see these stories as taking place in the same continuity, (even the really awful early ones), you could make the argument that the Duck Avenger starts out as personification of Donald's worst qualities; a role he adopts to do all the things he can't get away with in his normal life -- but over time he changes into a personification of Donald's best qualities; a role he adopts to help people in ways he couldn't as plain Donald.
And as such, the PKNA incarnation of the Duck Avenger is more or less the logical evolution of the character; perhaps he's been a little exaggerated, but he's more clearly than ever the personification of Donald's best qualities. (Which is probably another factor in why I have come to appreciate the Duck Avenger but find the DoubleDuck stories terribly boring. DoubleDuck plain doesn't have that interesting duality to him.)
As for the PKNA series itself... I don't know if I agree with the people who insist it's one of the best Disney comic series ever -- I think people who say that just stare themselves a little blind on the "darker and edgier" tone of the comic -- but it's definitely a solid series, and I would argue that it's among the best use of the Duck Avenger I've seen. If you're going to have Donald doing the masked avenger thing anyway, might as well take it all the way out and make it more of a superhero series with the traditional soap-operaish storytelling, prolonged action scenes and threatening villains.