Then why can't you choose to form cooperative relationships and communities on the basis of race without violating individualist principles?
I'm not sure what you're asking here, because I'm not sure what you mean by "can" or "can't" in this context. If you're asking why you don't have a right to organize or support or join deliberately racially segregated apartheid communities, then my answer is that you do have a right to do that: you have the right to be an idiot in many ways, and to do many brutally stupid things, including this one. I certainly wouldn't dream of using force to stop you.
If you're asking why you cannot organize or support or join apartheid communities that without facing severe social repercussions, ostracism, condemnation, etc., including from other people who are professed individualists, then the answer is that just as you have a right to organize or join a community based on something so brutalizing and idiotic as racial identity and ethnic segregation, other people have a right to call you an idiot, and possibly to sever social and economic ties with you, or to nonviolently protest you and your stupid racist community for doing so: they are exercising their rights to participate in consensual social cooperation, and dis-cooperation, just as you are.
If you're asking me why you should not organize or support or join apartheid communities then my answer is that you should not support them because if you do that, then you are deliberately and profoundly shaping your interpersonal interactions on a basis which is by definition brutally collectivist, judging people by the unchosen, completely worthless status of the ethnic group they were born into not by their individual qualities as unique human beings, their personal choices and actions, their chosen affiliations or their earned merits. This is stupid in obvious ways: I have much more in common in every way that is significant to my life as an intelligent and creative human being with fellow anarchists, philosophy students, former pizza-shop workers, Auburn alumnae, hackers, comic book nerds, Western swing fans, Trekkies and archivists than I have in common with some randomly selected jackass who just happens to share the same pigmentation level I do. But the reasons it is stupid are also intimately connected with the reasons it is anti-individualist: because it proposes to found individual identity and relations social solidarity on a set of unchosen, unchangeable, inherited and anonymizingly generic traits that have a great deal to do with historical systems of fairly brutal collectivist privilege, but nothing in particular to do with the individual personality. Now perhaps I am mistaken about the importance of individual personality; or perhaps I am wrong about the importance of chosen, idiosyncratic and personalizing social connections over unchosen, inherited and anonymizing social connections. But it should be relatively straightforward why as an individualist I am concerned about them. Perhaps I am wrong to attach so much importance to individualism; but then, what you asked is why an individualist would care about such things.
You may think racialism is idiotic, but I fail to see how it must be condemned on individualist grounds, seeing as it's just a way of organizing communities.
If you thought that the point of this article was to argue that any and every (non-invasive?) "way of organizing communities" is equally good, from an individualist standpoint, as every other (non-invasive?) "way of organizing communities," then I am afraid you have rather badly missed the point of the article. Certainly that claim was never made in it, and if you're now asking, I absolutely deny it.
My recent post On Being Pretty Much O.K. With That. (Factories, Corporate Secrecy, and Free-Market Anti-Capitalism Edition.)