Cleanup: explicitly disable autopep8 for rna_manual_reference

Currently the "exclude" option for autopep8 isn't as reliable as it
should be since passing in absolute paths to autopep8 causes
the paths not to match. See: D14686 for details.

So explicitly disable autopep8 in this generated file (the generator
has already been updated).

Also use spaces for indentation otherwise autopep8 re-indents them.
This seems like a bug in autopep8 since it's changing lines with
autopep8 disabled. Use a workaround instead of looking into a fix since
it's simpler for all our Python files to use spaces instead of tabs and
there isn't much benefit mixing indentation for scripts.

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