waste not, want not

season 6, "one small step"

it doesn't come up often, but whenever chakotay talks about his pre-voyager starfleet career, it's always about first contact or archaeology. in "emanations," he compares their exploration of an alien burial moon to a mission he went on as an ensign, all while demonstrating his anthropology expertise. add that to him nerding out in "blink of an eye," "one small step," the dinosaur episode, and a bunch of other examples, he's a social scientist both by training and by inclination.

in the original star trek, they had an "A&A officer," a specialist in archaeology, anthropology, and ancient civilizations:

tos season 2, "who mourns for adonais?"

we never hear that term again, but that's the role chakotay often fills on voyager, and he's very happy whenever he gets to do it.

now, realistically, i don't know how much time pre-maquis chakotay would have spent in a blue uniform, because those skills would not make him an obvious choice to lead a maquis cell. ro laren sets up his character (unnamed) in tng as a tactical specialist who resigns to join the maquis:

tng season 7, "preemptive strike"

(which is a very polite and noble way to do it, as compared to eddington's defection in ds9.)

if he was in fact ro’s teacher (i think so, despite a stardate conflict in some later dialogue), it seems very in-character to me that chakotay could have started out pursuing a sciences path before showing an aptitude for piloting, strategy, and/or command. given what we know of him, regardless of his own passions or preferences, if a senior officer noticed his skills and encouraged him to change career tracks, he would do it.

teen angst era aside, he respects authority. he argues against dogmatic ideology when it's inflexible to the needs of the moment, but he likes working within a command hierarchy, and for better or worse, he is easily swayed by charismatic leaders.

season 1, "caretaker"

not only does he yield to janeway's authority on voyager before she even asks him to, and then molds himself into the kind of first officer he thinks will help her most, he does the same thing with annorax in "year of hell." tom is the voice of ethical conscience and reason in that episode, and he organizes the rebellion—against chakotay's orders!

there's so much going on here:

season 4, "year of hell part 2"

despite his father's perceptions of him as a contrarian, chakotay only rebels as a last resort. he would genuinely rather not. he clearly talked about the maquis cause with ro and others before he left—and i bet that's why he resigned to a starfleet admiral in person, to make one last appeal. his preference is to try and change systems from within.

not to west wing about it, but chakotay is only The Guy when he has to be—he wants to be the guy the guy counts on.

(hot take: with how he rationalizes the calculated sacrifices annorax is making in "year of hell," i don't think chakotay would have left starfleet for the maquis if it wasn't personal. but it was personal, so here we are!)

maquis chakotay is a disillusioned idealist, but he's never that disillusioned. he believes in the stated ideals of the federation, sometimes more than janeway does.

season 3, "scorpion part 1"

and it's a fundamental character trait that he looks for the best in people and situations, often to his own detriment (tuvok, seska, annorax, that time janeway and tuvok and tom all lie to him for half a season, the list goes on).

and it's easy to see good in starfleet, especially when most of his career was during the height of federation utopia before "the best of both worlds," at which point starfleet remembered it's also a defensive force and started building the defiant—which was the very first starfleet ship ever designed solely for combat.

the cardassian situation in tng is shown as an aberration in a largely peaceful era. the off-screen "border wars" were fought by officers who expected to go their entire careers never firing a phaser.

tng season 4, "the wounded"

for decades since making peace with the klingons, and with the romulans keeping to themselves, starfleet has been mostly goodhearted nerds who are committed to exploring and making friends. even if chakotay was a tactical officer, that was the starfleet he signed up for and served.

and, in fact, the reason why the federation abandoned the colonists in the dmz in the first place and wouldn’t help bajor during the cardassian occupation is because the federation and starfleet are devoted to the ideals of peace and noninterference to a fault.

tng season 5, "ensign ro"

chakotay doesn't object to starfleet's actions, but its inaction.

which, side note, is why janeway's choice in "caretaker" makes it easy for him to rally behind her. by choosing to protect the ocampa, even though it's a huge sacrifice and puts her in a prime directive gray area, janeway specifically addressed the exact trust gap he has with starfleet.

season 1, "caretaker"

that's what he wanted them to do back home!

chakotay defends his starfleet uniform in the kazon scene that inspired this whole essay, and he believes what he's saying, because he's right: that's not what a starfleet uniform represents, either in theory or in practice. especially in the mid-24th century, regardless of the political issues, the federation and starfleet do not conquer planets or enslave alien cultures by force.

(of course, they wouldn't have helped the kazon free themselves either, but that's not the question on the table.)

to op's main question: it's an interesting (or boring?) doylist choice to make chakotay such a platonic ideal of a Starfleet Officer™️ (which, for the record, has always included going off-leash at the expense of one's career whenever ethics overwhelm regulations).

season 1, "prime factors"

star trek went to a lot of trouble to create the maquis for the voyager premise of two crews... and then quickly brady-bunch'd them into one happy family and let deep space nine wrangle the maquis problem instead. ¯\_(ツ)_/¯

chakotay being so willing to put himself and his crew into starfleet uniforms (even though some members of both crews objected to it) cheated us out of some potentially rich drama, but it does hold water with what we see of him as a character on screen, and his relationship with starfleet. it has disappointed him, but he still believes that it's a force for good, and chakotay will always err on the side of seeing the good in something and thinking he can change it for the better from within.

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tl;dr: chakotay is a starfleet officer by training and at heart, who was temporarily out of uniform because his family and tribe happened to be directly in the middle of starfleet's messiest ethical quagmire.