Bill gates was very involved with the code and structure of Microsoft's early software and this article basing its judgement of the two people on one email from Gates isn't exactly solid evidence that Gates was necessarily like that in person.
I do think the confusion was real. And it kind of makes sense when you think about it.
Bill Gates was very involved in Microsoft code, to the point where he used to review all code, even after Microsoft was no longer a tiny startup. He was a programmer, after all.
But that kind of thing doesn't scale. Especially when you have thousands of programmers, dozens of divisions all with "product managers", and many many products..
He obviously tried to stay in touch with Microsoft products as best as he could. But his role changed over time in his company - he could no longer be the chief code writer.
...and this was the fundamental failing of Microsoft. They were so involved in finding the next generation of revenue and growing (instead of just putting out dividends and cautiously expanding out of their core competency) that they lost focus.
Jeff Barr, the Amazon Web Services evangelist, mentioned during one of his talks that Jeff Bezos, the Amazon CEO, had an intimate hand in the shaping of the Amazon Web Services APIs.
However, I think there is a difference between Jobs and Gates that this illustrates: Jobs would do his best not to allow that kind of thing to ship.