In the near future, international space agencies have planned to achieve significant milestones in investigating the utilization of Global Navigation Satellite Systems (GNSS) within and beyond the current space service volume up to their application to lunar missions. These initiatives aim to demonstrate the feasibility of GNSS navigation at lunar altitudes. Based on the outcomes of such demonstrations, dozens of lunar missions will likely be equipped with a GNSS receiver to support autonomous navigation in the lunar proximity. Relying on non-invasive, consolidated differential techniques, GNSS will enable baseline estimation, thus supporting a number of potential applications to lunar orbiters such as collaborative navigation, formation flight, orbital manoeuvers, remote sensing, augmentation systems and beyond. Unfortunately, the large dynamics and the geometry of such differential GNSS scenarios set them apart from current terrestrial and low-earth orbit use cases. These characteristics result in an increased sensitivity to measurements time misalignment among orbiters. Hence, this paper offers a review of baseline estimation methods and characterizes the divergences and limitations w.r.t. to terrestrial applications. The study showcases the estimation of the baseline length between a lunar CubeSat mission, VMMO, and the communication relay Lunar Pathfinder mission. Notably, real GNSS measurements generated by an Engineering Model of the NaviMoon receiver in the European Space Agency (ESA/ESTEC) Radio Navigation Laboratory are utilized. A radio-frequency constellation simulator is used to generate the GNSS signals in these hardware-in-the-loop tests. The performed analyses showed the invalidity of common terrestrial differential GNSS ranging techniques for space scenarios due to the introduction of significant biases. Improved ranging algorithms were proposed and their potential to cancel ranging errors common to both receivers involved was confirmed.