So to simplify (correct me if I'm wrong), you claim there's a 'male principle/essence' and a 'female principle/essence' which are different aspects of divinity given to each person... and under these assumptions I can see why you'd infer a fundamental difference between each. And my understanding of theology is not even close to be sufficient to be able to engage with this on a, well, theological level.
Though I do have two questions:
First, you say "every rational creature is called into existence by one of the three persons of the Holy Trinity" (italics are mine). Yet so far you've only mentioned the son and the spirit. Logically that means there's a rational creature called into existence by the father; what would that be?
Second, I feel there's a contradiction between on one hand the idea of an essence, a fundamental quality which would necessarily apply to the soul, the very being of a person; and on the other hand the Y chromosome, which you call a "logical bifurcation", but which is purely physical and only a relatively small fraction of what makes a person a person. I'd say this mixes the spiritual and the physical levels in a way that is hard, if at all possible, to reconcile, which brings me to my next point, see below.
This is a little bit more tricky, but every individual either had at least 1 Y chromosome at the beginning of their life ( usually conception but it can be different for twins ) or they didn't. Its a logical bifurcation of sorts so to speak. So people with intersex bodies (as well as gender nonconforming people) would either be men called into existence by God the Son or women called into existence by God the Holy Spirit.
I'm coming from a biological background, and the sex of a person is so much more complex than merely the presence or absence of a Y chromosome. Splitting people into men and women is best understood as a societal model, a simplification which works well for most people in most situations. But as is often said in science, all models are wrong, though some are useful. The sex of a person is composed by different factors, including chromosomes, hormone levels, primary and secondary sexual characteristics, and while statistically speaking most of those traits will
tend to be either all male or all female, within a given individuum they can vary independently from each other (and often not in a binary way). After all, humans are living organisms, and diversity, in all aspects, is perhaps the most important characteristic of organic life.
For more on this, I can recommend watching
this youtube video (you can skip the intro, it's not relevant); it has a visually approachable presentation, and cites useful sources for further reading.
Point is, the reality of human biological sex is complex, as is gender (a social concept usually tied to yet independent of sex), and if you want your theological approach to be representative it needs to account for this reality.
