A time-based bounce rate measurement would largely minimize all the downsides listed in the article. (That plus some sort of event tracking for outside links.) It's unfortunate that's not the standard, default measurement for bounce rates.
In Kaushik's book, Web Analytics an Hour a Day, he defines bounce rate as "The percent of traffic that stayed on your website for fewer than 10 seconds." So that's probably why he's so keen on bounce rate, using his definition you avoid some of the issues listed in that article.
I don't think the 10 second rule minimizes all other points in the article.