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The closer you look at these things the more complicated they become. What we seem to know from the science is that:

• the brain is not entirely neutral, there are sexual traits,
• the sexual brain traits cannot be easily categorized into two boxes like "male" or "female", but are more like a constellation or mosaic of traits all in different configurations with very few brains fitting a category like "male" or "female", and
• trans women seem to share overlapping sexual brain traits with cis women, and it seems like this is true of trans men as well.

The science is just the current body of evidence we have, so we should expect our understanding to evolve as our evidence grows.

To more directly answer your question requires some clarification. It is unclear whether you're asking how subconscious sex relates to agender people (no sense of gender), or to gender fluid people (a changing sense), or detransitioners (sometimes changing sense), or even just any normal person, since none of us has that kind of direct access to our subconscious sex, it is implicit. If we could inspect it directly it would certainly make the whole "am I trans" or "am I a woman" question much easier, wouldn't it? Maybe someday we will have the technology, or maybe we will find that our concept of "woman" simply cannot be mapped to a complex biological trait like brain sex.

Subconscious sex is inferred, gender dysphoria and innate behavioral drives seem to give us footprints from which we can infer that subconscious sex from. Being a man and feeling the desire to wear a dress and skirt, how does he make sense of this? Maybe he assumes it's a fetish, but what if they enjoy it outside of sex, and maybe the sex when dressing up brings up so many complicated feelings (later she learns: dysphoric, even). Can it still be a fetish, can you be a crossdresser if you just want to wear a skirt around the house, but you have trouble extracting sexual pleasure from it? These are the kinds of investigating thoughts, the attempt to read between the lines. Some people might live their whole lives and never know their subconscious sex, they might successfully put off dealing with dysphoria or taking their crossdressing further. Some people have strong convictions from a young age and just know without as much ambiguity. There is quite a variety, just as the complex biology would imply.

It is also worth noting that it is a complicated relationship between something like subconscious sex or an innate brain sex and something like a self conception of one's gender. I certainly experience fluctuations in my self conception and even my felt sense of gender. Testosterone can make it much harder for me to feel like a woman. Moving through the world as a woman and being seen and treated as one by others creates a social circumstance that bolsters a psychological self conception as a woman. Neither of these things directly tell me my subconscious sex, but when the testosterone makes me feel awful, or when being treated and seen as a woman makes me feel wonderful, or when estrogen gives me mild waves of buzzing bodily euphoric, I make inferences about my subconscious sex from that.

So I don't know what you mean, but hopefully I have covered some of the ground you had in mind.