First of all, there is no such thing as "transition from male to female" ( or vice-versa ) in the real world. Simply put there is no way to alter neither the genotype or the phenotype to go from a fully functional reproductive male to a fully functional reproductive female. In that sense, Nyotaika as a genre is far from being a "transgender" genre ( with the only possibly exception of "Back Street Girls" and "Boku ga Watashi ni Naru Tame ni", which can be both considered a "transgender" manga ). Simply put if they do not have an XX sex chromosomes and have since birth the possibility to develop fully functional uterus and ovaries, they simple can not be considered as females from any rational point of view. Yes, due to a phenomenon of extended phenotype "trans-girls" ( some of them ) can look like like women and in some cases act like one, but they are far from being females. In a sense, if you buy that, you are doing nothing but buying a cheap knock-off of a female ( who also lacks reproductive capability ) instead of getting the real deal.
Now, regarding your Judith Buttler non-sense.... well, postmodernists are nothing but charlatans from the moment they reject the existence so something so obvious as objective reality, therefore debating the nonsense of postmodernism in this site would be a waste of time. For that there are far more better material that deals with the subject like "Fashionable Nonsense" and "Beyond Intellectual Impostures" of Dr. Alan Sokal or "Explaining Postmodernism" of Dr. Stephen Hicks. In that sense, those books are an excellent reference to understand the insanity of the ( false ) premises of charlatans like Judith Buttler.
Now finally, coming back to the original topic, the fact that in most Nyotaika manga there is a full transformation from male to female ( functional reproductive organs included ) up the genetic level really disqualifies them as being considered "transgender" stories. More so, most Nyotaika manga make a clear point on the aspect of sexual di-morphism like the difference in strength, muscle volume and height between males and females i.e. biological sex is not a "social construction" . Yes, there is the psychological aspect of the "heroine's journey" but that path is also heavily influenced by the push of female hormones in the new body and the way those hormones rewire the brain i.e also not a "social construction". In that sense, probably "Boku Girl", "Kanojo ni Naru Hi" and it's sequel, and "Tensei Pandemic" are a good examples of a good execution of such premise ( that the new body's female hormones push the rewiring of the character's brain ), even in the cases in which the protagonist initially reject those impulses. In any case, the point of the heroine being a full fledged female is the main distinction in most cases.