The morphing look is Superman being resurrected from the dead in the Fortress of Solitude by the Eradicator (renamed K in the later scripts). The resurrection goes back to Kevin Smith's original script.
Kevin Smith's script is still online and it's stated in there:
In Metropolis, inside the casket, the "S" on Superman's chest begins glowing red. Superman's body begins shimmering, and teleports (Trek-style) out of sight, leaving behind his suit, on which the security measures still blink.
In the Fortress of Solitude Superman lays in a Kryptonian resuscitation chamber. Arms folder over his chest, he is immersed in a gelatinous, green mass. His eyes snap open, and he sits bolt upright, breaking out of the dense goo. He throws up a lungful of the muck, inhales deeply. He slowly rises, wiping the jelly from his body and face. The old blue and red togs are gone, replaced by a black resuscitation suit.
My programming allows me to shape-shift into any form of equal mass to my own humanoid structure.
Building you a resuscitive suit -- your trial has left you injured and weakened. These units will expedite your recovery. This will support strained back muscles, these will repair the fracture in your shoulder, your ankles will need the support of this, this will protect your vertebrae.
http://www.script-o-rama.com/movie_s...es-script.html
All of the preceding Superman Lives scripts feature Superman being resurrected from the dead.
I don't know if any of the scripts specifically state in detail the appearance of Superman in states of resurrection. Tim Burton always has his own ideas for the way he wants things to look in his movies that are not always explicitly described in the scripts by the script writers but are evident in the designs, and the costumes created by Steve Johnson for Superman Lives.