Ohh I love this question! I too enjoy thinking about gender and gender theory.
In her announcement earlier this month Lilly Wachowski wrote
But these words, "transgender" and "transitioned" are hard for me because they both have lost their complexity in their assimilation into the mainstream. There is a lack of nuance of time and space. To be transgender is something largely understood as existing within the dogmatic terminus of male or female. And to "transition" imparts a sense of immediacy, a before and after from one terminus to another. But the reality, my reality is that I've been transitioning and will continue to transition all of my life, through the infinite that exists between male and female as it does in the infinite between the binary of zero and one. We need to elevate the dialogue beyond the simplicity of binary. Binary is a false idol
Prior to reading this I had been attempting to figure out why I the "trans- / cis-" dichotomy made me uncomfortable; Reading this piece caused my "Aha ha" moment.
I had been, as you seem to be, wrestling the idea that existence of "trans-/cis-" identities assumes a gender binary; In my line of thinking, the prefix "trans-" means "across something" and the word "across" implies there is some boundary to be crossed; A boundary creates two sides ergo binary.
Even if "trans-" didn't imply a specific boundary (Trans- continental doesn't mean there is a boundary in the middle of the continent), It does imply the existence of only two valuable positions; "trans-" as a term that at the least devalues the "middle" in favor of the extremes, and in the worst case denies the middles existence.
I don't think this attribute of the term "trans", is inherently problematic; I'm thoroughly convinced there are many people whose identities are well described by the terms "transgender" or "transsexual". I feel the problem is the fact that the dominant terminology is itself a new form of binary; A "trans-cis binary" which serves to reinforce the "male-female" binary.
Isn't this all labels? Is this worth getting all worked up over?
I think yes, for both questions. This is purely about labels and language; But language and language are important. Language is the limiting factor on thought, and idea that cannot be expressed in language cannot be thought; An identity that cannot be described does not exist. No one's identity should be denied existence.
People with non-binary identities, of which I consider myself a member, are devalued by the dominant "trans-/cis-" "male/female" binaries. I agree with Lilly Wachowski;
"We need to elevate the dialogue beyond the simplicity of binary. Binary is a false idol"
or maybe I'm wrong.