Lack of core stability is often what causes low back problems during a regular squat. The bar placement in the Zercher squat makes it a lot easier to activate the core and control the low back and pelvis. It's simply more natural (and real-life functional) to hold onto something in front of your body.
The Zercher squat is hands-down the best and safest way to squat, and it has more functional carryover than other bi-lateral squat variations. In fact, it's primal.
Squatting with a regular bar will often place the shoulders in extreme rotation, and if you frequently train heavy and never change bar type or placement, you might end up with shoulder pain – common among many powerlifters. This is one of the reasons why they use specialty bars in their training.
That said, the straight bar in the Zercher squat can be a bit tough on the forearms over time, so a zig-zag bar or even bamboo bar is a good choice if this is an issue.