I got a response from Apple through the feedback assistant that they fixed this in the latest version of iOS 17. I tried it out and it does work.
But there's still issues with models that has a combination of normal map/morpher/skeleton if one of these are taken out of the equation the shader seems to work fine and having all 3 of them breaks it.
I'm not using any 3rd party libraries to load assets I'm also not generate assets in code. Just loading Scenekit files and updating the shaders in code.