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The article only touches on it briefly but I think the difference between most issues and the few "gold-plated issues with megawatt cultural significance" is key. People saw Actions Comics #1 and Amazing Fantasy #15 selling for huge amounts and got the idea that #1 issues and first appearances were somehow inherently worth a lot of money, when in fact it's the cultural importance of Superman and Spider-Man that gave them their value.

Even if there weren't a million bagged-and-boarded copies of Rob Liefeld's Bludd Gunn McShootDeath and the X-Murder Y-Bunch #0.5 sitting in people's basements, it still wouldn't be worth anything because hardly anybody cares about those characters. Even classic runs from the 80s and 90s (Walt Simonson's Thor, Morrison's JLA, Sandman, etc.) haven't had anything like the cultural impact and recognition that major Golden and Silver Age titles did outside of comic circles.