No, the two went together for a very long time.

Because if the nature of your reality is that physical embodiment is an illusion and that all which really matters is what's inside you, then gender conformity isn't an important issue at all.

For example, this was a saying from an early 'heretical' tradition of Christianity which claimed that we are in a non-physical copy of an original physical world as created by an intelligence the original humanity brought forth (quite simulation hypothesis-y):

Jesus saw some babies nursing. He said to his disciples, "These nursing babies are like those who enter the kingdom."

They said to him, "Then shall we enter the kingdom as babies?"

Jesus said to them, "When you make the two into one, and when you make the inner like the outer and the outer like the inner, and the upper like the lower, and when you make male and female into a single one, so that the male will not be male nor the female be female, when you make eyes in place of an eye, a hand in place of a hand, a foot in place of a foot, an image in place of an image, then you will enter."

The idea here was that this realm is the copy of an original that we don't enter in some transition but are literally born into at birth (a rather radically different notion of "born again"). But this would necessarily mean that we are only in the image of the past, but are not foundationally male or female at all, as it's a temporary embodiment recreating the past.

The tradition's key point was to understand the nature of reality and in so understanding to realize that there will be an afterlife, but very close behind that point was pushing the importance of self-knowledge and self-truth:

But if you do not know yourselves, then you live in poverty, and you are the poverty.

So while yes, the notion of reality being simulated is a very big idea objectively, the subjective implications of that being the case are certainly tied to personal identity and in shedding the constraints of physical embodiment on how we define that identity.

Not really. Understanding gender stuff helped me figure out the nature of reality in several ways.

First, it made me realize that we don't have the freedom to choose what we want. We don't choose to desire food or water. We don't choose who we love or what gender feels right. I didn't choose to be trans, and I can't choose to be cis. Like not drinking water, I could avoid transitioning, but I'd die. If not doing something results in death, than there is no real choice on whether or not we can do it.

Second, I realized that we can never have certainty about anything, even what we want or who we are. I thought I was cis for a long time, and I didn't have total certainty that I was trans until I came out and felt better as a result. I didn't know I was a girl or wanted to be a girl, only that I wanted to be trans so I could be a girl.

Third, it helped me understand the true nature of evolution. It is the source of our very understanding of good and bad, right and wrong, but it is a cruel system of pain and suffering fuelled by blood sacrifice. Evolution, despite being the original good, is not good for individuals. Understanding "the good" tells us little about how to be good, ethical people.

I don't give a damn what our creator wants for us, it sucks. I feel a similar way about the Christian conception of God: I don't think anybody should look to a higher authority for their morals. There is no intrinsic good, only good from specific perspectives.

If all that doesn't touch on similar themes as the Matrix and its sequels, I don't know what does.