Which means that an engineer is a "loser" in this system; and in terms of monetary gain, they may very well be. The author stresses that "loser" is not the same as "bad person" or "living their life according to wacked principles".
That being said, the engineer position is also fairly privileged: the pay of a Silicon Valley engineer -- even if you take into account the standard of living (provided you live in a part of Bay Area that's comparable to most suburbs e.g. San Jose, rather than a hip part of SOMA) -- is more than middle management in most other parts of the country. The starting salary for a software engineer out of college can be as high as $75,000-$95,000. They can live a very comfortable lifestyle, where additional money (outside of "fuck you money") just brings diminished returns. This isn't true for many scientists (postdocs generally make a pittance).
Note that there isn't anything -wrong- with that. As you say, there may be reasons they do that, whether it is derived pleasure, or something else, but because they aren't actively gaming the 'ladder', they aren't going to move up it, and thus will always be losers.
I think this article works better, if you don't call them losers, and instead call them exploited, because there is such a strongly negative connotation associated with the term loser that it is hard to get past. The author is really saying that bottom layer is exploited (not compensated sufficiently).
Again, I want to emphasize that I realize these terms are shockingly harsh--and of course, if we're staying with this analysis, one or another of them applies to every single person in a (medium to) large organization. I'm trying to use them in a neutral, not inherently insulting way, even if that's almost impossible to do :) I'm just trying to extend the analysis of the article a little, and so I kind of have to use its terms (and of course, it wouldn't have drawn as much attention if it were phrased in a more neutral way, etc.)
It could be that the original article's analysis is just flawed, which I would consider a valid position, etc.--but I'm just going along with its terms because they do seem to fit shockingly well (to the point that the whole thing seems like a bit of a punch in the gut when I re-analyze some past experiences).