Last subtask from
https://github.com/paritytech/polkadot-sdk/issues/5704.

Closes #5704.

The substrate-node is not 100% free of the native runtime yet, but the
code has become less convoluted and better documented. The final cleanup
needs https://github.com/paritytech/polkadot-sdk/issues/7748.

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Co-authored-by: Michal Kucharczyk <1728078+michalkucharczyk@users.noreply.github.com>