No, not ALL of the Matoran Universe is made of protodermis, just the vast majority of it.
For example, Greg agrees here (https://greg.thegreatarchives.com/2008-2010/page287#post11477) that the atmosphere in the GSR is the same as the air that Spherus Magnans breath, since the Matoran/Turaga/Rahi didn't have any breathing issues when going to the island of Mata Nui, or migrating to Bara/Spherus Magna.
(Sidenote, as far as I know Greg has never confirmed what the Spherus Magnan atmosphere is actually made of, so it might not be the same as Earth.)
We know that the Scroll of Preparations (https://biosector01.com/wiki/Scroll_of_Preparations) is not made of protodermis, it's made of parchment.
Yes, almost everything else is just protodermis, including soil and plants. If there is organic muscle tissue made of it, plant-matter and soil (which is partly organic material) wouldn't be a stretch. (Personally, I headcanon protodermis to be a form of "programmable matter" that the Great Beings synthesised from the already highly transformative Energised Protodermis)
I don't have a source or solid memory for this one, but I'm 99% Greg would say that energy does not count. So the elements you mentioned wouldn't count as Protodermis, although Plasma and fire might be an exception, I'd be curious to see what Greg says about those.
(I do vaguely remember Greg saying once that a Toa of Fire has to generate something for the fire he controls to burn on, that's a very vague memory, idk of anyone could confirm that, because I guess whatever that combustible substance is would probably be a form of protodermis)