After several test flights using the newly placed waypoint, it was confirmed that the Navicomp only points to the center of the planet at close range. At longer range it points to the clockwise orbital entry point (the side of the planet where an arriving space ship enters a clockwise orbit). This was supported by the spatial inaccuracy between the waypoints.
Given the coordinates for HOM and GRN, the distance between them should be 1137. However at the midpoint between GRN and HOM the distance to each was 564 And 562, a total of only 1126. A distance of less than 1137 should not be possible if the Navicomp points to the center of the planets.
Flying directly at the express waypoint will put you in orbit around the other planet, despite not being aligned to the Navicomp indicator. The Navicomp indicator points to the clockwise orbital entry point, where the path through the waypoint uses a counter-clockwise orbital entry.
However, flying directly through the waypoint without a course correction is not recommended. A small error in the initial launch vector means that the spacecraft will miss entering orbit, or crash into the planet. It is recommend to apply a mid-course correction to align to the Navicomp indicator once it becomes available.