I think ignoring the fact that Transwoman Pre-OP x Ciswoman remains physically still hetero undermines the whole problem that comes with being a Transwoman.
I respect your personal identification with the "trapped in the wrong body" experience of gender identity, but your concern that the problems of trans women are being undermined by lesbians who fail to sufficiently dis-identify with their penis comes across as being based entirely on the offensive, even if well intended, idea of a single, authentic biological female body.
There is a general female body with typical sexual charakteristics. This is the whole reason why most transgenders inherintly wish to change their physical characteristics to the traits that are common among the gender they identify as. I wouldn't even call it an idendity anymore, but really a fundemental part of the sense of self a person has. Gender Dysphoria will be always an issue because it isn't as easily solved as homosexuality, where everything is right as long as the person has the legal fundation to have romantic or sexual relationships with their own gender, it will always need some medical treatment and it will always come with a disruption between the own sense of self and the body one is born with.
And in the context of Manga, it simply makes practical the most sense to distinguish between the romantic and emotional element of a relationship Pre-OP Transwoman x Ciswoman and sexual encounters, simply because most people want to see two physically tradtional female characters when they read erotic literature. In simple terms, nobody is looking forwards to see a penis and testicles when they watch or read lesbian porn. When people watch erotic stuff, the physical element is utterly important and Pre-OP Transwoman and Ciswoman simply doesn't fits the general expectation when somebody is watching this stuff. In such cases, if the character isn't on hormones yet, it is simply hetero because this is what we physically see, in an sexual intercourse between a Pre-OP Transwoman and a Ciswoman, we see nothing but a heterosexual act. If the Transwoman is on hormones and has already breasts and a already more female appereance, it is futanari, because in this cases, in the best case there is no visual difference between a futanari and a transwoman who still has er penis. In cases where the focus is on the emotional element, it's all different. In this case, we have the premise of a non-erotic Yuri, an emotional and romantic relationship between two woman, an approach on a different experience of lesbianism. Like, I don't think anyone would deny that Ayumi and Aika from Mermaid Line is Yuri, the focus is entirely about how Ayumi and Aika, two woman, come together and about their relationship with each other.