Wishbone: they created entirely new markets that didn't exist before
ET3D: Torchlight on the other hand played directly into an existing market. And yes, it "only" made about 1.4m sales, but that's not something anyone would scoff at. There are several indie games listed with over 2m sales (Trine 2, FTL, Binding of Isaac, Don't Starve).
Sure, but for every one of those games, how many others were released that failed miserably? For every market that exists, 100% market share is available, such is the nature of mathematics. But if, at any given time, 95% of the market share is taken up by 5% of the recently released games, then 95% of games are in deep trouble.
ET3D: Whichever way you look at it, the only point of the article is "you're not likely to sell much". That's something every indie dev knows, and it's true for pretty much all creative markets. That's a pointless point. Every creator knows it, and every creator hopes that their work would be in that tiny percent that makes it big.
Well, yes. But since money is on the line (game development is a costly business after all), then obviously a lot of people either have not actually understood that, or just have an abysmal business sense.
In order to succeed, a game has to have something special going for it. Either original ideas or exceptional implementation of existing ones. All of those games you listed have at least one of those, but the vast majority of released games don't. And those are the ones the article talks about, and not just indie games either, even though you seem to be focused on those.
The games the article talks about are those (the majority) that try to do nothing new, but instead try to gain a foothold on a playing field already densely populated. The ones that go for a specific demographic (as futile as that is), or a specific genre (using all the "tried and true" concepts of said genre). The end result is a game that isn't substantially different from tons of other games already on the market, and hence most of them fail.
The answer, therefore, is to do like the developers of the games you listed did, namely to make a game that they themselves would really like to play, because nothing quite like it already exists. As opposed to "Military Shooter #1736" or "Brutally Difficult Retro Indie Platformer #8462".
So no, the point of the article isn't simply "you're not likely to sell much". Rather, it is "if you try to compete in a saturated market, you're 99% certain to sell too little to make it worth your while, so don't do it". Really, if you want to boil it down to the bare essentials, the point of the article is "be original", and while it may seem an obvious truth, the fact that the
vast majority of developers don't follow it means that it certainly can't be obvious to everyone.