Masters can catch swords with their naked hands, the chakra catching the shuriken doesn' t have to be more durable than a standard body to be able to catch it.
Look at Metal Lee catching the shurikens of the best user of the classroom:
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For amaterasu, I don' t see why would Naruto ' s chakra would have to be more solid than a body to do what it did.
And you seem to forget that Naruto can control his chakra, he can make it more or less dense:
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And on the scan where Naruto is impaled, he is taken by surprise, meaning it certainly isn' t comparable to any damage he took in that mode while knowing he was going to be hit.
There is no debate, what I say is fact, Yata hype is still hype, it is just a matter of when you' ll accept it.