That is by design:
From the fftw manual:
FFTW includes multi-dimensional transforms for real data of any rank. As with the one-dimensional real transforms, they save roughly a factor of two in time and storage over complex transforms of the same size. Also as in one dimension, these gains come at the expense of some increase in complexity–the output format is different from the one-dimensional RFFTW (and is more similar to that of the complex FFTW) and the inverse (complex to real) transforms have the side-effect of overwriting their input data.