If one reads the definition in DataGen or in the 'input lines' in the Tow manual one expect that XYZ-TOW-coordinate system implies that roll is about X and pitch about Y of one's SACS-model-coordinate system and not that the Z-axis flips downward changing the expected outcome. The manual tries to explain and warn but it doesn't. This doesn't work intuitive and introduces errors. Please see also Case CS0371438.
The Tow coordinate system input in Tow is intended to support motions from different coordinate system conventions. Standard coordinate systems for vessels are XYZ where +Z is pointing down. If you want to use a motion coordinate system with Z pointing up, use the default coordinate system YXZ. And if you want to rotate the structure relative to the vessel, use the POSITION line instead of changing the Tow coordinate system. Changing how the Tow coordinate system the way that you suggest would limit the different coordinate systems that are supported and would force users to transform the motion data they get from their Naval Architects.