You have a choice in this matter. If it's fun music you like, it can be found if you do a little digging.
Problem is that most indie music is just as trite and formulaic as chart stuff. Usually, it's just timbre, production and performance that's different. Mostly, the structure, tonality, melodies and harmonies are very, very similar to chart music.
If I had a nickle for every supposedly underground song that could be turned into a chart hit with the right production and marketing, I'd be a supergazillionaire.
I can understand the point you're trying to make here (after all, enough marketing $ made a hit out of Modest Mouse - something I would not have predicted) but the more I consider it the more I disagree.
First off, if you change the "timbre, production and performance" of a song you're changing the song. Radically. You act like these are just minor tweaks, but put Bob Rock on a song instead of Bob Pollard and it will be a completely different song. The band will receive different direction, both the execution and the elements of the song changes. Nirvana's 3 albums are a high-profile case study of this.
I also notice you ignore lyrics in your analysis. Which to me is one of the defining differences in indie music, while they can be just as underwritten they rarely pander with marketing-focus-group patter like the pre-packaged stuff tends to do.
I mean - the structure/melodies of the Supremes, the Ramones, and Hanson are similar but they couldn't be more different from an execution standpoint.