Graphene p-n junctions offer a potentially powerful approach toward controlling electron trajectories via collimation and focusing in ballistic solid-state devices. The ability of p-n junctions to control electron trajectories depends crucially on the doping profile and roughness of the junction. Here, we use four-probe scanning tunneling microscopy and spectroscopy (STM/STS) to characterize two state-of-the-art graphene p-n junction geometries at the atomic scale, one with CMOS polySi gates and another with naturally cleaved graphite gates. Using spectroscopic imaging, we characterize the local doping profile across and along the p-n junctions. We find that realistic junctions exhibit non-ideality both in their geometry as well as in the doping profile across the junction. We show that the geometry of the junction can be improved by using the cleaved edge of van der Waals metals such as graphite to define the junction. We quantify the geometric roughness and doping profiles of junctions experimentally and use these parameters in non-equilibrium Green's function-based simulations of focusing and collimation in these realistic junctions. We find that for realizing Veselago focusing, it is crucial to minimize lateral interface roughness which only natural graphite gates achieve and to reduce junction width, in which both devices under investigation underperform. We also find that carrier collimation is currently limited by the non-linearity of the doping profile across the junction. Our work provides benchmarks of the current graphene p-n junction quality and provides guidance for future improvements.