I have always struggled to ply from a center pull ball. I am in awe of the folks that can do it effortlessly. I have trouble getting the same amount of tension on both plies, I even have trouble holding the ball because I have small hands.
The thing that makes my eye twitch about center-pull-ball-plying is the uneven twist. The ply that comes from the center gathers more twist as it unspools than the ply that comes from the outside of the ball. To my eye this leads to an inconsistent yarn. Even if I do get the tension even on the two plies, one is a little tighter twisted than the other.
The photo shows the phenomenon exaggerated because the tape is flat and was wound tightly, but it's a good illustration.
I don't knit my handspun from the center strand either, unless I want a little more twist in it. I do knit quite frequently from the center when I knit with commercial yarn. I think most commercial yarn is a little underplied, so I am happy to add a little more ply when I knit from the center of a cake.
This is just another one of those personal preference things, but the more you know about your yarn the happier you'll be.