We haven't added any feature to ImageAugmentationLayer, but I don't see any reason why you shouldn't be able to achieve what you want by using the "generator" syntax of NetTrain as I mentioned in my old reply. Your generator function should grab a raw image together with its mask, generate random cropping parameters, apply the same cropping to both image and mask and return the crops.
ImageAugmentationLayer
NetTrain
In the meantime I'm using this function to do it.
randomCrop[is_, sz_] := Module[{x = RandomReal[{-1, 1}], y = RandomReal[{-1, 1}]}, ImageCrop[#, sz, {x, y}] & /@ is ]
