What is in the realm of religion is imagineering a gendered brain into the mix
I'm not sure I'm interpreting what you're trying to say correctly, but the way I'm interpreting it, there's nothing particularly implausible about it.
From a biological and evolutionary perspective, to the extent that we agree that behavioural phenotypes aren't entirely learnt, and to the extent that they (or individual aspects about them) show a bimodal distribution rather than a single overall mode with different means for the sexes, it's entirely plausible that occasionally, due to a rare coincidence of environmental, genetic and epigenetic factors (none of which has to be individually rare), an otherwise phenotypically normal male with intermediate or more female-typical neural structure is born (or vice versa), not entirely unlike occasionally we get otherwise phenotypically normal males with undescended testes, or partially fused labia.
It is even entirely plausible that this happens significantly (possibly even orders of magnitude) more frequently in humans than in other apes - comparing the patterns of of sexual dimorphism in our species with those of our closest relatives, it becomes obvious they have been under significant selection in recent times, and it's at least plausible that we haven't reached a new stable state yet.
It is even plausible that we
have reached a near-stable state, but that stable state continues to produce more such individuals than in other apes because our males have been bred for lowered androgen sensitivity,
in particular in the behavioral/neural/cognitive domain - the phenotype evolution was handed when it started this particular project the outcome of which are human males is that of a testosterone-laden hulk with self-control issues (for reference, typical chimp males, orang males, gorilla males are all just that). This just isn't the most successful phenotype in a species as social as ours. That's obviously true in 21st century America, but it remains true in much more patriarchal, warlike societies. Triggering a blood feud in the course of which half of your brothers and agnatic cousins die is hardly going to improve the inclusive fitness of a young man in 19th century Albania, for example, even as the precise location of the sweet spot is going to differ. The only
easy way to reduce the incidence of that maladaptive phenotype is to shift the lever for androgen sensitivity during neural development all the way to the left, but with a background of overall genetic variation and variable environmental factors, this
will almost certainly produce a tail of individuals that fall well outside even that "new male" selection target and within less than a standard deviation of the female and. Quite plausibly, since relative to other apes, the male phenotype is the one that has mostly evolved to be more "feminine", this will happen at rates much higher than the inverse scenario.
Given that the selection for lower androgen sensitivity/expression in males was almost certainly driven primarily by the cost of their
behavioral effects given the environment of our tight-knit social structure, it is even entirely plausible that this happens
substantially more often than, say, unfused labia in males. To the extent that the latter are more common in humans than in chimps (no idea if they are; no idea whether we know), for example,
that could be the side effect of selection for a less expressed masculine
behavioral phenotype. Remember, as a rule of thumb, biology is messy and dripping fluids that better remain unnamed from various orifices. There is no one "gene for male aggression" that evolution can just select a weaker variant of and be done. There's dozens, maybe hundreds, of genes that influence the androgen sensitivity of various pathways during neural development, few of which are going to be selective in that they
only affect neural development, but
all of which are going to selected for up to the point where their maladaptive effects in other ways, or the occasional cases where they coincide with other (individually selected for) genes in a way that produces a maladaptive phenotype, outweigh their positive effects that have made them the target of selection. And for some of those genes, the "other effects" (besides affecting neural development and its androgen sensitivity) are going to be lowered androgen sensitivity elsewhere in the system.
I don't claim that any of that is true. I don't know how much research has been done that could confirm or falsify each of these hypotheses. What I do know is that they're all well-formed hypotheses within the paradigm of evolutionary theory, and - dare I say it? - plausible ones in the context of what we know about the recent evolution of humans, and about sex differentiation in primates and mammals more broadly. Unless you are privy to actual research that tested those precise hypotheses and found them lacking, calling them "religious imagineering" does not reflect well on your understanding of evolutionary theory.
and then arguing that such speculative minds supercede the phenotypes that define our sex.
I don't know what "supercede the phenotypes that define our sex" means, but obviously, behaviour and cognition
are part of our phenotype,
even if they were entirely learnt (in that case they're simply a part of the phenotype that is dominated by environmental factors - in biological terms, a cultural context is just another part of the environment). And "supercede" in what context? In the context of determining whether an otherwise male person with a more female-like cognition thinks more like the typical woman or more like a typical man, there is no need to argue for it at all - it's a tautology!