Georeferencing using ground control points (GCPs) is the most common strategy in photogrammetry modeling using UAV-acquired imagery. However, with the increased availability of UAVs with onboard GNSS RTK, georeferencing without GCPs is a promising alternative. However, systematic elevation error remains a problem of this technique. We aimed to analyze the reasons for this systematic error and propose strategies for the elimination of this error. Multiple flights differing in the flight altitude and image acquisition axis were performed at two real-world sites. A flight height of 100m with vertical (nadiral) image acquisition axis was considered primary, supplemented with flight altitudes of 75 m and 125 m with vertical image acquisition axis and two flights at 100 m with oblique image acquisition axes (30° a 15°). Each of these flights was performed twice to produce a full double grid. Models were calculated from individual flights and their combinations. The elevation error from individual flights or even combinations yielded systematic elevation errors of up to several decimeters. This error was linearly dependent on the deviation of the focal length from the reference value. A combination of two flights from the same altitude (with nadiral and oblique image acquisition) was capable of reducing the systematic elevation error to less than 0.03 m. This study is the first to demonstrate the linear dependence between the systematic elevation error of the models based only on the onboard GNSS-RTK data and the deviation in the determined internal orientation parameters (focal length). Besides, we have shown that a combination of two flights with different image acquisition axis can eliminate this systematic error even in real-world conditions and that georeferencing without GCPs is, therefore, a feasible alternative to the use of GCPs.