My thought is that protodermis is a specific unique compound or element, but then nothing in the Matoran Universe is made of pure protodermis.
For example, Protodermic rock is a mixture of protodermis and minerals from Spherus Magna.
Liquid protodermis is a slurry of water and protodermis. (This also fits with the idea that the oceans and rivers inside Mata Nui were for transferring materials)
Protosteel is an iron-protodermis alloy.
Tren Krom is protodermis-infused strawberry Jell-o.
And so on.
This also explains why Toa and other Matoran Universe beings are able to use their powers on non-protodermic beings or objects: their powers were designed by the Great Beings to work on the non-protodermic version (perhaps using technology developed by the Great Beings prior to the concept of the Great Spirit Robot), but then they homogenized the Matoran Universe with protodermis to strengthen the connection between a being and the object they are manipulating.