The crop numbers are unit-less. They are a ratio, in the way that a camera may shoot 3×2 or 4×3 – those are also not in mm or pixels.
6″x9″ is not well defined either, because it depends on the ppi and images are simply in pixels.
If you want a 6×9, which is also 2×3, then set the crop to 2×3 and when you export, specify the size you want in pixels.