"twys" more than anything is a strongly preferred guideline, not an unbending rule. It would actually cause more problems if we didn't have a few exceptions, and besides, if we rejected the concept of "otokonokos" then we'd experience constant arguments and tag wars over tagging characters like Astolfo as girls despite canonically being guys.
If we can tag Astolfo as a guy because that's what he is canonically even though there's nothing visibly distinguishing him from a girl, then why can't we tag Hibari as a girl since that's both what she canonically is and what she appears to be when clothed?
Do you mean we should tag them as newhalf, which would also tag them as futanari? If you're goal was to cause a neverending shitstorm over mislabeling trans people as futas, I couldn't suggest a better way to do it.
I'm not saying I agree with newhalf implicating futanari- personally I think more useful would be to have some cover term meaning 'any woman with a penis' that both implicate. But as long as it does it seems like an okay solution that at least tags trans women as women while allowing people who don't want to see penises to not see penises.
In general there is no visual difference between a flat chested newhalf and an otoko no ko, so the otoko no ko tag gets priority by TWYS. I could even say that newhalf are technically otoko no ko with breasts. If the character has noticeable breasts, newhalf usually get the priority (unless it's manboobs).
Not saying that I agree or that this is my view IRL, it's just how danbooru tagging works.
But if canon can supercede TWYS for clothed otokonoko with nothing to visibly distinguish them from girls, why can't it supercede it for flat-chested trans girls with nothing to visibly distinguish them from otokonoko?