With my expirience with custom skins', this seems to be the game recognizing the texture image, but unable to use it. I've only seen this when expirimenting with a preinstalled paint program, and an older Minecraft version. aparently that program atomaticaly uses a transparecy layer. Also when I tried opening a world when using that broken skin, the world wouldn't load, and told me the current skin was missing, or corrupt.
It's not restricted to void worlds, and the respawn anchor doesn't need to be fully charged. You can immediately fix the issue by placing a block in that space, but then the block you placed is lost and the ghost block returns to what it was before the explosion.