The size-based separation of electrophoresing DNA chains of various lengths in microfabricated obstacle arrays (Volkmuth and Austin, Nature 1992) and self-assembled arrays of superparamagnetic beads (Doyle et al., Science 2002) has recently been experimentally established. The chain dynamics in these devices have been modeled previously (Minc et al., Phys. Rev. Lett. 2005; Dorfman, Phys. Rev. E 2006). However, previous studies do not fully take account of the electric-field dependence of chain extension that is observed in experiments (Randall and Doyle, Macromolecules 2006). In this study, we extend the continuous-time random walk model of chain dynamics in the obstacle array with account for incomplete chain extension. In addition, we evaluate the accuracy of the model by performing Brownian dynamics simulations of DNA chains of different lengths in a self-assembled array of magnetic beads at various electric field strengths. We provide predictions of chain mobility and dispersivity in the device, and the resolution achievable among chains of different lengths.