I would say that while the historical Cao Cao comes off more ably and as (somewhat) less of a jerk than in the novel, especially since his SGZ biography isn't preoccupied with depicting him as a villain, in the way that the novel does, the reality is that the historical record is not without distortion or bias, either.
In particular, the accounts of his remarkably small armies and yet impressively thorough accomplishments against Yuan Shao and sons in the north are almost certainly embellished. Much as Pei Songzhi and others note in the annotations to the bio, it would be impossible for Cao to have completed some of the achievements he is said to have done if he had really had such small forces.
So, yeah, the novel is definitely twisted in one direction, but Chen Shou had a Jin ruler breathing down his neck and the Jin were eager for the Cao-Wei dynasty to be seen as having the Mandate of Heaven since they usurped the Cao-Wei. If not, then their own dynasty would be invalidated, as well. So, I don't think it's a surprise if we note that the original historical record is biased in a different way.
Fortunately, we have Pei's annotations to help curb some of this but then you also get the issue of ambiguity. Historical Cao Cao is muddier and less easy to define than Novel Cao Cao, partly because we get multiple different versions of events. The story about him killing his uncle (while not reflecting his ability as a ruler) has several different versions as does the bit with Tao Qian and his dad. And if you read through you'll notice certain authors/sources have consistent opinions. Sun Sheng for example always has something contrary to say about Cao Cao (and, indeed, other Cao family members as I am discovering with Cao Pi).
So then you have to weigh up who you believe because ultimately everyone is biased - Chen Shou, Pei Songzhi, the various sources selected by Pei for the annotations - it's simply a question of to what degree and how much does it interfere with the veracity of the account. Personally, I buy the opinion of those arguing against some of the details of Chen's account of the conquest of the north because there are 3 or 4 of them and only one of Chen, and their arguments make sense. But it jsut kind of depends on the situation.
So - yes. There are differences but there are also differences within the historical record itself.