In such situations, how does one distinguish a male with bad intentions from the others, though?

That they may insist on access to spaces they know are intended to be female-only, despite being well aware that many women are uncomfortable with this male imposition, is already an indicator of dubious intention. Perhaps not directly predatory, but certainly a violation of boundaries.

I don't think that an advanced stage of transition can broadly override this, in reality. Becoming a modern type of eunuch isn't the same as actually being a woman. It seems unreasonable to compel women to accept these as being equivalent.