Real Fast Fourier Transformation (FFT) in 2D changes with changing the axes order
A real, 1D DFT is fully described by the non-negative frequencies, since real DFTs are symmetric about the 0 frequency bin.

The function you linked is only computing the FFT along one dimension, and is only returning the non-negative frequency bins.

From the manual page:

"Notice how the final element of the fft output is the complex conjugate of the second element, for real input. For rfft, this symmetry is exploited to compute only the non-negative frequency terms."

You can use symmetry to fill in the other half of the result, if you need it.