I'm not on Linux, I'm dual booting but I performed the installation on my windows side. I'm having trouble finding that video, would you mind linking it?
Hey my dude! See that shouldn't be causing any issues. Lets see about fixing this. The install instructions and video are here:
https://mrkane.itch.io/aperturereconstructed
And it's worth noting that the MD5 for Media.zip should be: 8AB4E954A0F235F61FAD46CD2152D5B3, so if we can get things to a known-good state by this step we've excluded a whole stack of problems already. Good luck, and don't be a stranger because I'll add a few notes to the guide when you do figure it out!