Yup. Cis and trans are simply Latin anotonyms, literally meaning “next to” and “across from” respectively, and since nonbinary people are not cisgender, they are transgender.
A tangential word of warning from an amateur philologist: this reasoning is treacherous. Our wonderful language is full of word pairs which, from their prefixes, would seem to be antonyms, but aren't: "access"/"abcess", "concern"/"discern", "compute"/"dispute", "incite"/"excite", "inspect"/"expect"... See if you can find some of your own! It's fun! ...if you're a very particular kind of geek.
EDIT: And even in the case of antonyms, well, an "ingress" may be an entrance, but an "egress" is not "anything that is not an entrance". Antonymy is not always exhaustivity.
More topically, it seems weird to apply this binary logic of "If not X, then Y" to, y'know, nonbinary people. Granted, logic is logic, and a binary is impossible to escape at some point -- "nonbinary" itself could not be more explicitly a binary term -- but still.
Ehhh, aliens speak to each other in English when no humans are present to hear them in cutscenes in that game, so I don’t assume the writers put quite that much thought into the possibility of translation errors. But even if we assume that there is some degree of English having insufficient vocabulary to accurately communicate the nuances of the Krill caste system, I would still argue that the choice to “translate” their pronouns differently depending on the stage of life the subject is in is an indication that there is a concept at least roughly analogous to gender associated with caste and morphology at play in their society.
It also sounds like they may be sequential hermaphrodites (I know nothing of the game other than what you have described). If so, the "concept at least roughly analogous to gender" may simply be biological sex, or tied to biological sex or reproductive function. Or the pronouns could be assigned by the human translators on that basis -- would hardly be the first time. They might not make the gender/caste distinction in their own grammar at all. (Which is not to say that they can't make the distinction very heavily in other areas. Turkish is a genderless language, but Turkey is hardly a genderless culture.)
This is one of the things I love about fantasy. It gives us the frame of reference to ask questions like “would trans-ness still exist in a culture where gender was traditionally chosen rather than assigned?” despite such cultures not existing in real life.
Well, the greater implication of the question is "Will trans-ness still exist in
our culture as trans rights continue to make strides?"
I would say that yes, if elves did not assign genders to their children, elves would not be trans within their own culture, but could be trans to people from cultures that did have more rigid gender norms. For example, let’s assume that in Eladrin culture, it is considered normal for personalities to shift dramatically with the seasons, and the blessing of Corellon is at least common knowledge if not common occurrence, and so they never developed a cultural concept of “men” and “women.” An Eladrin who finds themselves preferring what humans would consider male sex characteristics but exhibits personality traits humans would consider feminine probably wouldn’t develop a strong sense of identity connected to womanhood or manhood, because those just aren’t part of their world. However, if this character made a trip to the prime material plane and encountered humans, those humans might have preconceived notions about this Eladrin based on their physical appearance, manner of dress, and behavior. They might be surprised to learn that this Eladrin is “male,” because of their own cultural gender constructs and related biases. Upon learning how humans view gender and sex, this Eladrin might even incorporate this new perspective into their own sense of self. They might be inclined to refer to themselves as a “woman” around humans, because they find this (admittedly foreign) concept more closely aligned with their identity than that of a “man.” In a human-dominant society, they are for all intents and purposes trans, because their identity as it relates to that culture’s concept of gender does not match the gender that culture’s norms would ascribe to them based on the culture’s own criteria. It’s effectively like having a gender assigned at contact with another culture, instead of at birth.
Hmm. It seems to me like you're still implicitly attributing them a gender identity, despite the stipulation that they don't have one. The humans call them a "man", and if they don't line up with all the human norms for that label, so what? They don't line up with human norms in a lot of ways, and never expected to. But referring to themself as a "woman" in contradiction of the label assigned them implies they have a preference in the matter. Doing so to the likely confusion, consternation, and possibly even hostility of the humans implies they have a
strong preference.
Say a human enters, oh, dwarven society, and finds out that they have defined social roles for
unak and
khivud dwarves. When she asks what these words mean, she is told "right-handed" and "left-handed". Now, this human is right-handed, but her behavior more resembles that of
khivud dwarves. It strikes me as more likely for the human to accept the translations and write off the social expectations associated with
unak as a dwarf matter than it is for her to challenge the definitions of words in a language that is not her own and the norms of a society that is not her own for the sake of a concept that is not a part of her own identity and is unlikely to become one. A dwarf, acculturated to feel that
unak and
khivud are important, might well be motivated to carve out a place for himself as "right-handed, but
khivud anyway, they're not actually the same thing". An outsider, though? Anything is possible, but I think dwarves expecting a human to care about whether they call her
unak or
khivud would be projecting their own attachment to those concepts onto somebody who honestly doesn't have it.
(Corollary question: Are
unak and
khivud genders?)