If they need to go thru checkpoints then they are not trespassing their territory. If that's the definition for apartheid then the US border control with Mexico should be taken down for second thoughts.
Regardless to that btselem is an opinionated pro-palestinian organization, at least from the first 3 examples in the source they show biased information. The cities they mention and Hebron in particular, is divided between Israel and the Palestinian Authority by the 1996 agreements. From the nature of such division to get directly from one point to another might be impossible in some roads, yet there are other roads leading to same point, so no 2 points are totally disconnected.