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The Spirit Transformation doesn't make Dan intangible, it allows Dan's soul to leave his body. The soul itself IS immaterial. That's it.Only the ghost transformation jutsu makes the soul intangible via databook. Rinnegan users pull souls out so they can have the feat. Itachi’s spiritual weapons are intangible by statement. Chakra as a whole is not intangible. None chakra users can use, see, and interact with chakra in boruto. There's a human scientist experimenting chakra technology.
As for Naruto, he literally grabbed his soul/life-force/chakra and did a tug of war against Kurama and Nagato. Both of these acts have been noted as similar in nature by Bee.
He later did another tug of war for the Bijū's chakra against Obito, again using chakra arms.
Also, as pointed out in the OP, Madara's soul existing his body was referred to as chakra. There are many other examples of this in the OP