That would be an acceptable explanation for Naruto finally kneading a Rasengan with a single hand, without the aid of Kage Bunshin, additional arms, and chakra shrouds.
The way they originally set up the hurdle of difficulty when it came to adding Nature Transformation with such a high level of Shape Transformation made it out to be a matter far beyond simply "gittin' gud"; I'm sure you understand that. :p Otherwise Kakashi wouldn't have phrased things the way he did.
It may very well be the excuse they end up using. But I don't think it makes very much sense.
First, when Kakashi said it'd be impossible for him, it's not improbable that he meant in his state when he said it, as opposed to just something he straight up would never be able to do.
Second, it is perfectly conceivable to me that Naruto became able to do all that stuff with one hand no matter how big of a deal was made originally due to the fact that through his usage of Shadow Clones to handle each different step, his mind got a better understanding of how each individual step works and through doing that for years, combined with the fact that he retains memories/feelings/experiences from the clones and that he got a feel for what his easier control looked like under his various forms, he'd be able to eventually replicate those results alone and with one hand. Usage of those clones in the first place allowed him to get an understanding for years of chakra experience in just a couple days before the Kakuzu fight. It'd make sense for his mind to just reach unprecedented levels of understanding on the intricacies of chakra control through continued usage of his clones when performing the techniques for the years after that initial pre-Kakuzu training. I doubt Naruto would be able to teach it but considering the way he fights and the way his body is set up to learn in an OP way, the guy possibly has the equivalent of decades upon decades upon decades of chakra experience.
(Edit: And if it's not conceivable to you, just imagine he pops out tiny Kurama chakra hands on his palm whenever he does something and those handle the different steps lol)