I think this article has a stupid definition of meritocracy. If I work really hard digging a giant hole in my backyard and no one pays me for it, few would agree that "meritocracy is dead". The article argues that there are programmers "as good as" Bill Gates that didn't become billionaires, but don't acknowledge that Gates never let being a good programmer get in the way of being a great business man. In doing so, I think they make an equivalent argument to the "digging holes in backyard" guy. Being merely a good programmer is insufficient to become a billionaire.
The article in no way says that being a good programmer is sufficient to become a billionaire. It states that there were long-shots and coincidences that led to Bill Gates's stellar rise as Microsoft's founder, beyond his programming and business skills (It's not denying that his programming and business skills didn't contribute). The article states that, in competitive contexts, many have merit (programming + business skills, in the context of Bill Gates), but few succeed. What the article is effectively trying to say and the point you seem to miss is that, the the link between merit and outcome is tenuous and indirect at best.
In new and fertile territory (random) variations that offer small (unforseeable) advantage can and often do dogpile until total victory is achieved, but I would hardly say the rest of the field flounders. Populations of 1%er's begetting the next don.
>If I work really hard digging a giant hole in my backyard and no one pays me for it,
If I work really hard and with people with same interest and nobody pays me for it. At least I've made good friends