These should be the same, except with one less dimension. They are not.
> ts.genetic_relatedness(sample_sets=[[0, 1, 2], [3]], indexes=[(0, 1)], windows=[0, 5, 10])
array([[-0.11970621],
[-0.122826 ]])
> ts.genetic_relatedness(sample_sets=[[0, 1, 2], [3]], indexes=None, windows=[0, 5, 10])
array([[-0.11970621, -0.13156656],
[-0.11175358, -0.122826 ]])