The article is saying not to mess with the "religious" tradition of i/j/k, which means that the author actually things that ii/jj/kk are better. I don't think it's hard to follow, really, unless maybe if English isn't your first language.
Actually later on in rule 20 he implies (with negative logic of course) that i is actually a good inner loop variable name. So that's an inconsistency right there.
index, jndex, and kndex, are preferred, obviously.
I mean - I don't recall writing a loop longer than 2 screens in years. Usually a loop is less than half a screen long.
And anyway, you can search for [^\w]i[^\w] if you really need to.
Maybe it's aquired taste, but in array-heavy code (usually math-related) I much prefer A[i][j][k] * B[j][k][i] than the same with long names for index variables.