One of less often mentioned characteristic trait of Touhou songs including original Bad Apple!![1] is that, at least to me, it more resembles a data bus status display than music; it makes a lot more sense to imagine it as listening to even bits of a 16-bit bus tied to instruments as MS-DOS boots, than music with regular tempo and musical measures. That's to be expected as these songs were created for hardcore PC-88/PC-98 shooter games by the developer of Touhou games all by himself without formal education in musical theory. I think that makes it rather familiar to embedded hardware engineers than most other music.

Another factor is nicovideo.jp / nico-tech community developed from 2ch/futaba culture. Lots of users with way more domain expertise than pay or financial ambitions threw in their skills into remixes for fun(many were STEM students back then). Unidentified FPGA wizards, motor driver experts, video editors, would just come by and drop psychedelic videos. It was absurd. So absurd that Maker Faire Tokyo once put suspected nico-tech dress-shirts into a quarantine zone in a separate venue to save face for ambitious t-shirt webdevs(that was naughty, and lead to creation of nico-tech meetups, and also was never repeated). That absurd content quality-quantity density sure had created inertia for Bad Apple!! PVs.

Undoubtedly one last key element was that the PV was monochromatic(okay, grayscale). That's probably why it wasn't one of other ones from the golden age of nicovideo.jp.

1: https://www.youtube.com/watch?v=Yw5HTeT_dis