This reaches all the way back to Hagio Moto and Takemiya Keiko’s work (and, to a lesser extent, Ikeda Riyoko's) in the ‘70’s.
Sorry, but this isn't quite true. I'm actually sort of boggled that you said Ikeda's to a lesser extent, since she is the one that really deals with the most GL-themed stories out of the three.
Having read nearly every single work of Hagio Moto's, I can tell you point blank that her three favorite plot devices tend to center around "gender identity" (specifically playing with the idea of transexuality in futuristic settings), "twins", and "male homosexuality". Unless there is a one shot out there that has elluded my grasp, I can't think of a single story in which she's really dealt with f/f [sub]text. Takemiya, on the other hand, while I'm not as familiar with her stuff, I know that she has done GL work. As has Kihara (of the classically underrated Mari and Shingo series fame), and of course Yamagishi, who started the whole GL shebang.
Going back to Hagio for a moment, while she might have used boys instead of girls as originally planned in Touma no Shinzou, the cause is a little more complex than "these were originally supposed to be lesbians and thus should be read as such". One, both she and Takemiya were inspired by a particular European movie about a boarding-school-romance-gone-badly involving two very male protagonists--this accounts for the similarity in theme between Kaze to Ki no Uta and Touma no Shinzou (though Touma is really the more subtle work, which is why I prefer it). Two, Hagio has always been more comfortable with male protagonists--it's a theme that can be traced back to all three of her "major" stories, and something she has confirmed herself in interviews. I'd also be hard pressed for you to read something like Zankoku na Kami ga Shihai Suru and come away with the idea that the protagonists are just "girls in boys clothing".
Your essay also ignores the evolution of the BL genre in general, which I find sort of saddening. No, liking BL does not make you a tolerant person, but BL as a whole has been sliding towards "more realistic" for the past thirty years as it gets more attention and better authors as mangaka dabble in it. Yamada Yugi might be a good place to start. Or even try reading HaruDaki--which starts as BL of the most ridiculous shade and then, over the decade in which its been serialized, has grown beyond its roots into something that was the top pick as a homosexual manga by a homosexual author (whose name sadly escapes my memory at the moment, I apologize) in the 2006 edition of "This Manga is Amazing".
Don't get me wrong--I'm more of a lover of classic 70's shoujo then I am BL, which is why my ire was slightly raised by your essay, which I think simplifies the history of the matter far too greatly and assumes too much on the half of those interested in the genre. While I appreciate your warning and think many could do with it, I think the reasons people enjoy BL are as varied as the types of people themselves.