The set phrases "a few choice words" and "some choice words" have a more interesting past than I had imagined. Originally, the wording was used to indicate an especially pleasing bouquet of words, as, for example, in this instance from Vernon Lushington, "On Learning by Heart," reproduced in Class-Book of English Poetry (1866):
For those, in particular, whose leisure time is short, and precious as scant rations to beleaguered men, I believe there could not be a better expenditure of time than deliberately giving an occasional hour—it requires no more—to committing to memory chosen passages from great authors. If the mind were thus daily nourished with a few choice words of the best English poets and writers; if the habit of learning by heart were to become so general, that, as a matter of course, any person presuming to be educated amongst us might be expected to be equipped with a few good pieces,—I believe it would lead , far more than the mere sound of it suggests, to the diffusion of the best kind of literature, and the right appreciation of it, and men would not long rest satisfied with knowing a few stock pieces. ....
From M. de Betham-Edwards, The Sylvestres, serialized in Good Words for 1871 (1871):
Had the history of this gold chain been clearly made out, Ingaretha was certainly the original owner of it; but, in Monsieur Sylvestre's eyes, it mattered little how he came by a thing, so long as he had the pleasure of giving it away, and consecrating it by a few choice words, a hand-clasp, or, better still, if circumstances allowed, a kiss.
And from "The Books of 1884," in The Publisher's Weekly (January 31, 1885):
The late Dr. Ewer's sermons were issued in book-form, with the title "Sanctity and Other Sermons;" a selection of Talmage's most important sermons is embraced in the "Brooklyn Tabernacle ;" and some choice words of Beecher's in "Comforting Thoughts." Savage's "Beliefs About the Bible" is a Unitarian's inquiry into the divine origin of the Book.
But at some point, English speakers latched onto the expression as an ironical or euphemistic way to refer to naughty, harsh, denunciatory, brazen, or otherwise unsuitable-for-polite-company words. Thus, even as early as Ruth Sheldon, Scraps (1898), we have this instance:
A little boy of four, who had been out to play with older boys, and had picked up some choice words, said as his mother put him into his bath, "Jesus Christ, this water's hot!"
And likewise from Bill Mauldin "Books and Men," in The Atlantic, volume 180 (1948):
Several Catholic dignitaries made angry mutters about the picture, and the Brooklyn Tablet, which has stanchly supported Father Coughlin's Christian Front, and which suspects everybody but the toughest conservative of being a communist, ran a front-page editorial about the cartoon, with a headline stating that the New York Herald Tribune (a steady Republican paper) was going pink because it had printed the drawing. Several organs of the Knights of Columbus reprinted the Tablet editorial, and added a few choice words of their own.
It's the first time in my life I have been so roundly cussed in print, and I reacted as do most people who make a career of poking at other people and who suddenly find that they have to put up with a little of what they dish out; I didn't take it so well.
From Proceedings of the Annual Convention of the National Association of Animal Breeders (1970[?]):
I have some choice words for certain temperaments [in milk cows] I do not think lend themselves to top production. Mean, goosey, scary, timid, and stupid are a few of them. I use other words when I speak directly to these cows. The ideal temperament is alert, friendly, and gentle—in other words—a pleasing personality. Cows must be aggressive in their eating habits.
And from West's Southern Reporter (2000):
Suppose instead of speaking among friends, one goes to a theater to watch a movie but finds the movie uninteresting, gets up to leave and while doing so employs some choice words that we all could agree would be vulgar, to describe the movie, but the words are not directed at any particular individual.
Clearly the uplifting sense of the original use of "some [or a few] choice words" has been subverted in a number of later cases by the subsequent euphemistic use. And yet both senses of the phrase continue to appear in print. Under the circumstances, to interpret the sense of the expression in a particular case, you must take into account the context in which it appears.
In the poster's example, the phrase "you’ve learned some choice words for people who do that [namely assume that a hypothetical or generic person whose gender has not previously been specified is male]" probably means "some choice words" in the sense of "some highly critical words." But every situation is different, and here, more context would make an accurate interpretation easier.
(As a matter of fact, you can find the entire original text that the poster asks about at Scott Alexander, "SSC Gives a Graduation Speech"—and from that longer piece it is evident that " – this time I’m assuming you’re a man, I’m sure over the past four years you’ve learned some choice words for people who do that" is an aside to his audience of graduating college seniors, who have been attending college for the previous four years and are presumably attuned to gender-based assumptions and criticisms thereof.)