Once the system is bled and the lever is squeezed, all of the hydraulic pressure is equalized. All pistons are fed equal pressure regardless of the 'over-the-fender' setup. It is simply not true that the pressure starts on one caliper before the other.
The real reason to use two individual brakelines is that they are easier to bleed. There are no "traps" where air bubbles can congregate. Other than that, the 'over-the-fender' brakeline does have the advantage of less unsprung weight and easier routing.