When writing a geotiff writeGeotiff always adds a ModelPixelScale even if a ModelTransformation is present. This results in a nonconforming output file.
Per spec:
The next two tags ModelPixelScaleTag and ModelTransformationTag are optional tags provided for defining exact affine transformations between raster and model space; GeoTIFF files may use either, but shall never use both within the same TIFF image directory.