How can protodermis have so many different forms and varieties, from molten to metallic to “water” to organic?
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Maybe it’s like carbon where it has many different allotropes, like when the particles have a different arrangements, they take on different properties.
Also keep in mind that Earth rules do not apply here, except when we want them to. Protodermis is an artificial substance, created in a lab, so the GBs simply made sure it had the properties they needed it to have,.
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I figure it’s probably a programmable material that responds to certain signals (electrical, perhaps) to shape itself in certain ways, with some properties being enhanced by alloying in impurities to produce stuff like protosteel. It would be an incredibly powerful building tool, but beings made of it would also be vulnerable to all manner of ‘misprogramming’ powers, which provides some groundwork for the sheer number of mutagenic powers that exist in the Matoran Universe.
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So, like those guys above said, it could be considered a “smart” substance that could take on numerous forms with the proper stimuli? Their ideas would certainly explain the way things like Pit Mutagen can affect MU residents so rapidly while organic creatures are affected the way they would be on our world.
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It’s magic
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Protodermis being programmable to a degree would also certainly explain how the Makuta could use vats of protodermis and viruses to create Rahi and mutate existing lifeforms, like Mutran with the Shadow Matoran (including that one that ended up half-Rahi) and the Shadow Leeches.
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It’s nanomachines. 
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I personnaly see it as a material that can transform and mimic in any possible natural element by a mean that only Great Beings know.
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Protodermis is part of Mata Nui’s body. Ga-Metru filtered it, I assume as part of the robot’s bodily functions. Pretty sure it’s in his skin, too, hence ‘dermis.’
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