Series artist Daniel Cabuco would ultimately clarify the intended role of the eggs as an unused boss mechanic:
"Well we went thru a lot of ideas with the Zephon battle. One was that there would be a small group of human hunters who made it there (you can see the flame thrower of one that was left behind). If Zephon grabbed one and 'ingested' him, his next egg would hold a fledgling Zephonim. But the stress on the ps1 and the player would have been too much (AI and player frustration would be too high) so we nixxed all the humans and left the exploding eggs as our primary mechanic."