When you fight the Lavos Spawn, do they have tiny space engineers in them?
Lavos takes the power and traits of things on the planet it feeds on (retroactively through time, I guess)I'd assume it starts as just the shell with the fleshy bit up front growing inside the shell into the Cell and Frieza guys by feeding and assimilating
Lavos is basically banking on you targeting the most obvious threat and it didn't realize that you've spent the whole game fighting bosses that use similar tactics.