I did verify that HyperSizer does not support beam orientations that are not in global coordinates. The orientation vectors must be defined in global coordinates.
HyperSizer DOES correctly interpret beam orientations that are defined by a GRID reference.
By the way, even if HyperSizer does not correctly interpret the orientation, it will not affect the analysis or sizing if you use "neutral axis" reference plane on your beams on the Sizing Form | Options tab. In that case, there are no transformations to be done either on import of FEA loads or export to the FEM for iteration. If you use one of the other options (Beam Top or Beam Bottom), then the offset vectors exported by HyperSizer to the *.CL1 file will not be correct.