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Twitter themselves had a guide that explained why NPR and BBC were not labelled as such> "State-financed media organizations with editorial independence, like the BBC in the UK or NPR in the US for example, are not defined as state-affiliated media for the purposes of this policy."
That explains the what, not the why. It says they aren't going to consider BBC and NPR as state-affiliated, but not why they aren't going to consider them as state-affiliated. "Editorial independence" is a meaningless superlative that cannot be empirically measured through any means available to twitter.
The "why" is because the "state affiliated" label was meant to be innuendo for "untrustworthy" and twitter, under previous management, did not consider NPR and BBC untrustworthy.