Hello @blue_sky,
Based on the description it appears that the problem is with saving the non-image, RTStruct, DICOM data. SimpleITK supports operations and IO for images and you should be able to correctly save the results in DICOM format (see this example).
Saving the RTStruct is not supported by SimpleITK, so possibly use pydicom (see this discussion), dedicated tools such as RT-Utils or Slicer’s Slicer RT extension which enables this form of DICOM export.