It's simple enough - grunge and emo weren't "underground" but were commercial music, aimed at a wide, conventional audience, using the same chord progressions, song structure, timbres and time signatures that have been part of music since the 1950s.

Is there really some great difference between "Louie, Louie", and "Smells Like Teen Spirit"?

Here's an example of a piece of underground music from that period. Yes, the Butthole Surfers later had a couple of radio hits, and good for them, but there was never a time where "The O-Men" (above) or "Cherub" were mainstream.

And it wasn't just them. Bands that were underground twenty years before that are still underground today. No one's going to be playing the brilliant Mona: The Carnivorous Circus on your typical radio station even today, and there's no way that Merzbow will ever get a Grammy.

And finally, yes, there are huge numbers of underground movements that are alive and very active today that will never emerge to your average listener.

As an example, noise music has been around for fifty years, and now has a vast range of different sounds and artists, and yet even the most poppy noise music (like "7 ➡ (Boriginal)" by the Boredoms, one of my favorite songs ever) will never get wide play - but the Boredoms sell out large concert halls.