What are the consequences of Madeline Wyndzen's critique of autogynephilia?
You have presented a critique of Blanchard's model that clearly shows methodological flaws and the over-interpretation of data. But, in the end, have you done anything but weaken the model a little? Couldn't everything you say be addressed with future research? Until then, why shouldn't we accept Blanchard's model? It's not very satisfying to say we don't know what to think. Despite its flaws, maybe it's the best guess we have?
I get the impression that you interpret choosing a scientific theory in the same way you would choose a presidential candidate. Unlike votes for president, there is no election day. We can remain agnostic as long as need to without bad consequences. Sometimes that is best because it helps us think broadly about new directions to explore. By philosophical tradition, scientists are skeptical. We try to remain neutral until evidence gives us a strong reason to choose one belief over another.
Still, scientists like me share your need to have a theory and search for evidence to support it. You are very right to point out that many of my criticisms can be addressed by future research (e.g., adding control groups, treating age as a covariate). That's part of my point! When you think scientifically, you have to be open to both evidence that supports or refutes a hypothesis. I am open to the possibility that more evidence could become available to support some hypotheses in Blanchard's model.
Some of the points in my critique show that the evidence is inconsistent with Blanchard's ideas. The scatter-plot of sexual orientation looks nothing like what we would expect if there were two categories of transsexuals. Similarly, J. Michael Bailey and Anne Lawrence bend over backwards with post-hoc  explanations to dismiss the BSTc findings.  Furthermore, if a mis-directed sex-drive really causes gender dysphoria, then medicine that reduces the sex-drive (like in hormone-replacement-therapy) should reduce gender dysphoria. It does not. Ray Blanchard explains away this problem by saying transsexuals form some sort of "pair-bond" with the women they hope to become. This is like how the sexual spark in marriage declines over time and is replaced by a stronger emotional bond. There are obvious questions this raises. If it's really so, how come boot fetishists don't reach a point where they become emotionally attached to their boots, feeling safe and comfortable with them, even without being aroused by them anymore? It's been over a decade since Blanchard gave this post-hoc explanation and we still have no plausible evidence for this "pair-bonding." These post-hoc explanations are necessary to support the two key points in Blanchard's model: two categories of transsexuality and a mis-directed sex-drive as the eventual cause of transsexuality. With such little evidence and so many post-hoc explanations, I have trouble considering Blanchard's model intuitively plausible.
Implicit in my critique was a model of transsexuality you could hold instead of Blanchard's. It's actually so common-place, many people probably don't even realize it can count as a theory. Let's call it the "gender identity conflict" model. I'll describe it using two hypothetical male-to-female transsexuals (it applies to FtM TS too):
Gender dysphoria for Glenn and Steve has some distal unknown cause (e.g., maybe pre-natal or early childhood experiences). Like many other boys who will grow up to be gay, Glen is feminine in childhood. He tries with some success to fit gay culture and through his experience quickly finds the drag scene. Those experiences clarify for him what his gender dysphoria is about and he transitioned to Gloria is his mid-twenties. She lives happily ever after. Just like Glen was like other gay boys, Steve is like other straight boys. Steve tries with some success to fit straight culture. He chooses a career in computer science sub-consciously because you can be androgynous but also not violate straight-man norms. Androgyny doesn't relieve his gender dysphoria, he still doesn't understand it (often thinking of himself as "just" a cross-dresser) and he increasingly fantasizes about the woman he wishes he were. In his early-forties he finally decides that he needs to relieve his gender dysphoria in a way that isn't just coping with an escape into fantasy. He transitions to Sarah and she lives happily ever after.
In short, this model says that gender dysphoria can cause transsexuality and circumstances (like gay and straight culture) are part of what guides the path transsexuals follow to find themselves. This model is consistent with Blanchard's data. There are no "types" of transsexuals even though sexual orientation correlates with many things (like cross-gender fantasies, childhood experiences, and age of transition). Moreover, unlike Blanchard's model, this model explains why transsexuals feel identity is so important and why the cross-dressers in Blanchard et al (1986) had some underlying gender identity conflict.
Blanchard's model is only supported if you: (1) ignore methodological flaws, (2) over-interpret data, (3) accept post-hoc explanations without evidence, and (4) treat as unimportant the inability to explain why transsexuals feel their experiences are about identity (aside from adding yet another post-hoc explanation by calling transsexuals liars). Alternately, you can hold as a starting point a "gender identity conflict" model for transsexuality and let your scientific curiousity take you on to a more thorough explanation.
Footnote 1: "Post-hoc" means "after the fact." In scientific contexts, it means that when a theory has trouble explaining something, you make up a plausible corollary to fill in the gap but you keep the basic theory the same. There is nothing wrong with post-hoc explanations, in and of themselves, though it's much nicer to explain novel findings with predictions from your theory, "a priori." Post-hoc explanations become a problem when no new evidence is found to support them and when there are so many post-hoc explanations that it makes the theory itself seem clunky rather than elegant (the fancy scientist language for an elegant theory, without clunky corollaries is "parsimonious")
Footnote 2: This is a finding about a part of the brain called the BSTc. Men and women have different-sized BSTc but people of different sexual orientations do not have different sized BSTc. That made it a plausible biological correlate for mental phenomena "gender identity." In a study, the size of the BSTc in male-to-female transsexuals was like other women. Transsexuals of different sexual orientations and ages of transition did not differ in the BSTc. These findings suggest the BSTc may be a genuine biological correlate of gender identity and these findings are inconsistent with the idea that there are categorically different "types" of transsexuals. Michael Bailey and Anne Lawrence offer the post-hoc explanation that the transsexuals in the study were "really" autogynephilic (despite data on their experiences to the contrary) and so this is just a possible correlate of paraphilia (even though it's correlation with "gender identity" was an a priori hypothesis).