The argument seems fairly straight-forward:

Twitter has a definition for what they consider state-affiliated media. NPR doesn't fit this definition. Thus, if they brand them as state-affiliated, they are not going from their own definition, and they must have other reasons.

Why is it acceptable for Twitter to have a definition of state-affiliated media, and then apply the branding to a media organisation that doesn't fit this definition?

Or are you just saying that there isn't a difference between state-affiliated media, and state-funded media?