More importantly, where did they get the skulls, and why isn't "where did the Flaming Lips get the human skills they used as album packaging" like the number one question on Quora?

Probably because Tetsuya Nomura is running the show now. They've had a winning formula for about 20 years now with him providing all the character designs and they probably don't want to change that. I personally would be happy to see a Final Fantasy game again with characters that don't look like Japanese teen pop…