Some of it is fretboard knowledge, like that video you just posted (how to play the same chords we all know and love in different ways). Other times it comes about due to experimentation. Don't discount different tunings, even different stringings (Nashville tuning, or even the crazy stuff done by
Sonic Youth--not mentioned on this page is that custom string sets were used for almost every different tuning).
One thing that popped into my head was the English Beat's "Save it for Later". For years, I played that in a band, and got by passably with a Dsus2 (xx0230) for that first chord but I always knew it wasn't exact.
Turns out, Pete Townsend was trying to cover the song, and trying to get it right completely flummoxed him. So he called Dave Wakeling. Turns out, Dave was playing his guitar in DADAAD... flipped upside down and played left handed! Yikes!
https://www.youtube.com/watch?v=xTWChIJxOiY