I use the dragonfire pass through bezels in my stock seats, and they work perfectly. The bezels themselves leave a little to be desired as far as installation and fit, but there not horrible. I also have custom cage and the cross bar is raised slightly compared to the stock one.
It definitely beneficial and more comfortable to have them pass through the seats as opposed to have them running around the outside of the seat and riding on the edge of your shoulders. Ideally, the harness should run over the top of your shoulder and be perpendicular to your shoulders, or at a mild downward angle.