I'm under the impression that most subcultural music genres are motivated by the fact that the people behind it have some kind of aesthetic preference that the pop/rock mainstream doesn't really cover. Maybe it's just on the aesthetic/stylistic level, maybe they don't really resonate with what the music stands for in terms of the deeper conceptual themes and philosophical ideals behind it. The point of most subcultures, not just those that revolve around a particular style of music,  is for people dissatisfied with the mainstream to create their own culture that functions from ideals they can make sense from - either to do so separately from the mainstream, perhaps with the hope of later influencing the culture at large into a course they find agreeable. 

The ideological aspect is in my experience more important to people from places like Eastern Europe, Latin America, South East Asia and the more religious parts of the United States... again, referring here to the metal/punk side of things. In North America and Western Europe, the outer shells of the subcultures co-exist with the mainstream where they mutually influence each other. The underground "harder cores" of the subcultures, the ones referred to in the essay linked to in the OP, are exclusive by design. They're the ones most willing to build up basement distros and do-it-yourself concert venues and whatnot, because they feel the least at home in the cultural mainstream hence being least willing to compromise with outsiders... basically they've got a kind of "patriotism" about their respective subcultures. The subcultural elites of are as a result rather suspicious towards outside influences, or new members that come in because they might not completely understand or even appreciate the ideals of the community, perhaps just appreciating the superficial without having to go through the experiences that a full on commitment would entail, most so the case when the respective subcultures become popular. 

This is where that Letter to the Underworld essay comes into relevance, because it means the genuinely dedicated in the underground end up going against each other instead of standing together. The woman who wrote it is not just an industrial/noise musician, but also a veteran of feminist/LGBT activism and oldschool hacker culture... she's in particular annoyed at the latter two coming into conflict with each other in recent years, when she finds both at risk of mainstream co-optation and wants them united against that front. As a result, her experiences with subcultural cannibalism are very harsh. (this might also explain why she frames the whole thing in a political angle)

Where the "art music" world comes in is that it's often drawn from people who also are dissatisfied with the popular culture, but perhaps from different backgrounds and dissatified for different reasons. To start with, as a result of being intertwined with academia and cultural (sometime also economic) elites it's made by and for people with higher social status than the general public. The subcultural art/music scenes, on the other hand, tend to attract people who are lower in social status. Either it's because they didn't really have that much of a choice in the matter, because of things like social class or ethnicity or sexual orientation etc... or because they've actively rejected the frames. Sometimes it's both... see the author of the essay I discussed in the last paragraph as an example, the goth/indus/noise music scene seems to be disproportionately LGBT.

Now, the avantgardes of the art music community and those of underground art culture as shown in the music subcultures I've mentioned do sometimes end up borrowing from each other, through artists who happen to be on both's wavelengths. The fact that they are willing to think outside of box because they value different things than mainstream culture means that they're more likely to come up with... as a result, those willing to "compromise" between the mainstream and both high culture/sub-culture might be responsible for keeping the mainstream culture evolving. Think of mainstream culture, high culture and underground culture as a 3-circle Venn Diagram in this regard.

This is why while the subcultural patriotism I referred to earlier is a mixed blessing. On one hand, the subcultures might end up dying completely or fall apart if everyone distrusts not just new members but also each other for not being "true". (I already mentioned the intersection with politics earlier in the thread, which is an interesting tangent to keep in mind but I'm not sure I can really do that justice right now) On the other hand, there also needs to be a hard core who maintain some distance because they keep the flame burning, offering different perspectives from every other cultural community. An example is that metal's golden age in the 1980s and early 1990s came, or punk's a bit earlier, about because the underground back then was exclusive enough to only let in those who "got it" but also good enough at rewarding interesting new music coming out within the framework of that culture.

As far as the question of how often countercultures in general, and those related to music in this regard, actually live up to their own declared ideals, goes... it is my conclusion those are rare occasions. This does not mean they aren't good ones to strive for. It's debatable how many progressive/psychedelic rock groups had that much of a coherent ideological/philosophical concept beyond "let's fly into space", with groups like Amon Düul II or Henry Cow or The Mothers of Invention (Zappa in general?) or Magma being the exceptions. Nor how many of them synthesized classical and jazz into rock music beyond more the use of outside technical flourishes in the context of rock songwriting, again it's something that I get the impression that Beefheart/Zappa/RIO-style avant-rock and Krautrock (or "Kosmische Musik") was better at integrating compositional structures into something genuinely new than the classic Anglo-prog. Indeed, beyond Beef and Zap the avant-prog stuff is not something I listen to very often, and even in their case there are large stretches of their discography I haven't gotten around to listening... often including their most celebrated output. Krautrock I now listen less to than newer electronic music inspired by the scene. This does not invalidate or mean good music can't come out of it without fulfilling those lofty goals, indeed said mythic ideals of the underground music might be more useful as abstract Platonic ideals to strive for with only the rarest few actually achieving them, but can still impact people's lives opening them up to new directions as well a second-hand inspiration towards not just more avant-garde and highbrow music forms, but also new artistic/literary inspirations and philosophical/religious/political ideas. I've also gotta admit that I at times admire the avant-garde of art more through its second- and third-hand influence on more accessible stuff. It's not that often I have enough brain capacity to process really "highbrow" stuff.

I know I did touch on the sociological/political aspects of underground music without exploring them further, something I might have should have done especially now that I brought up punk. At the end of the day, though, the fact that I don't find most underground music subcultures fulfilling their own proclaimed ideals very often means that it's a long time ago I've actively identified with them. Perhaps being that kind of active participant just requires even more time and commitment than I've been willing to expend, so the option of not dropping in on the "formative experiences" of an underground subculture is one option I might not really have had that much in a pre-internet age? I might explore them in a future post I'll make later this week, perhaps where I also summarize the conclusions I made here in this post. (and could provide more concrete specific examples) 

Think of this as first draft of my own conclusions. My next post might start with a summary of this one. I really should start a blog of my own one of these days.