attributing it to the brother of Jesus lacks strong historical evidence. Its dating and origin are subjects of scholarly discussion,

The authorship and dating of all writings are subjects of scholarly discussion. Suggesting that it is "more so" with Thomas is ludicrous. No one agrees on anything.

and it likely emerged from a different theological milieu than the canonical Gospels.

Did they come from a different "Theological" milleu? Maybe. But the key word there is "theological" (belief system about the fundamental underpinnings of reality). That doesn't mean they didn't have a common original source (the teachings of Jesus). Maybe it was just that some people (disciples of Saul) felt that some things fit better with Saul's teachings than others did, so they labeled them as heretical and forbid people from looking at them. I mean, the winners literally burnt the books. How can you not appreciate that?

That Saul had a larger impact on the Christian Doctrine we got than Jesus did is not really debatable (though I wouldn't be surprised if you try). Why do you not appreciate how large of an impact he had? He was a self proclaimed Levite Agent. The person personally responsible for the Martyrdom of Stephen, not to mention very likely numerous other deaths of "heretics." Almost every single piece of Doctrine that exists today (a notable exception being the Trinity) comes from Saul's interpretation, or as you call it, "Theological explanation" of what "God" is to him, not from Jesus himself.

As I said, all of the red letters of Jesus are decidedly in congruence with the gospel of Thomas. If you find "discrepancies," I suggest it is through the theology of Saul and the later doctrine from the Constantine Church that you make it not fit.

This saying emphasizes the seeking of hidden knowledge that leads to a higher state of understanding.

It suggests that by looking inward (meditation) we can find an appreciation of Reality. It is by looking inward that we will find our Connection to Source. This is completely consistent with other teachings found in Canon (from Jesus, not from Saul's interpretation).

This saying introduces a Gnostic theme of transcending gender for spiritual enlightenment, reflecting a departure from traditional Christian teachings.

The focus on gender wasn't "Christian," it was cultural (both Jewish and Roman culture, though especially Jewish, which became Christian culture as well). Saying "she will become male" likely has more to do with suggesting "all people are created equal." They are created equal, in the sense that all people, no matter their station, accomplishments, strengths, gender, whatever, are all equally connected to the Source of All Things. Sounds to me like a pretty good idea.

Just because all people are equal (in the sense given), doesn't mean there aren't differences. You are applying a smaller scope, under your understanding of "equality," as presented to us by the Cabal, to something that is actually rather profound. It is true that we are all equal. It is also true that we are not the same. They are just different "Truths in scope." They are only at odds when you try to force one scope onto the other. That is what the Cabal does. And you are falling for it.

This saying encourages a deeper, metaphorical understanding of the Kingdom of Heaven, emphasizing spiritual insight over literal interpretations.

And what in the red letters suggests otherwise?

Having said that, this goes along with the general theme of all teachings of Jesus that is the understanding that the Kingdom of God (the Jurisdiction of Source) is everything (Reality). If there are different "realms," or "dimensions," or whatever within Reality, then that is how it is. There is nothing here at odds with those ideas.

It's important to note that the Gnostic flavor in the Gospel of Thomas lies in its emphasis on esoteric knowledge

What is "Gnostic?" It is a box where you can place things to discredit them, nothing more. A teaching is what it is. Putting it into a box is only done as an association fallacy. It has no place in reasoned discussion. Not to say it's easy to not do that. We have definitions for a reason. But in this case it misleads from the discussion. "Gnostic" is just a word that means "to know." It means to know the teachings of Jesus in this case. It wasn't about hiding the knowledge (as suggested by the word "esoteric"). It was about trying to show people the knowledge that was hidden from them by the dogma of the time.