It depends on the figure. Some, like the QmX Trek figures, tend to have sculpted necks so that joint is hidden. Custom figure creators now often think carefully about this when they release a sculpt. HT's default is to do a separate head because it means more flexibility in posing. But some of their figures, the Godfather comes to mind, also had a sculpted neck.
But putting that aside, most figures will have something that distracts them from "reality." If not a neck joint, then maybe a wrist joint, buttons that are too large, etc. It's all subjective, but I think it's particularly noticeable on something like Spidey where he has a cloth piece connecting head to neck. The first Spidey figure from HT (Spiderman 3) actually didn't have a separate head piece, but it had other issues.