I think he explains what he's saying in the video, but it takes about 3/4 of the video to get there. When he de-tunes his C-string and plays the chord, it very obviously sounds dissonant. Even to my untrained ear, it sounds bad. When people say, "I've never heard this song before?" what they really mean is that they don't know if the bad sound they are hearing is intentional or not. If you watch a lot of Rick's other videos, you know he has not only a trained ear but also an understanding of chord sequences. Even if he hadn't heard the song before, he would know that a chord sounded bad based on what notes were played before it.
To your last point, Rick's thought is that people /should/ be more sensitive to out-of-tune-with-themselves instruments given how perfectly tuned most commercial music is these days, and that's why he's surprised that people don't hear it (or think that it might be intentional).