Slicer can certainly read DICOM RTSTRUCT and save it as a labelmap in Nifti format.
By default, when you export a segmentation to a labelmap volume, Slicer uses the smallest necessary image extent, so the input grayscale volume’s geometry will not be the same as labelmap volume’s. If your software requires the grayscale and labelmap volumes to have the exact same geometry then you just need to specify the grayscale volume as reference volume for labelmap export (see Segmentations module Export/import… / Advanced section).