SCNMorpher seems to want just the difference between the source and target vertex position, whereas Maya stores blendshape data as originalModel.vertexposition + whatever the displacement is.
I havw quickly solved this by writing a Maya script that does this. The blendshapes look wrong in Maya but they work just fine in Xcode. Not the ideal solution but good enough for now.
I'm currently dealing with exporting blend shapes from Maya to Xcode and running into this as well. I'm curious exactly how you're using your MEL script to export the blend shapes and if you're able to get consistent results in Xcode/SceneKit.
Alex, can you pleas post the script?