Raw energon is a metamorphic rock.
I can explain. Metamorphic rocks are formed when a protolith (base rock which is either sedimentary or igneous) is subjected to immense pressure and/or heat. The g1 cartoon had a depiction of liquid energon being formed by compressing different forms of energy. (Weird cartoon logic where you can do that to oil and electricity if it's in a special box). Other cartoons show a more solid crystal like energon instead. I believe shifting tectonic plates (in a universe with transformers) can cause lingering energy in a planetary body to crystallize. I headcanon it's more potent than an artificially created liquid energon once it's refined because of the energy actually used. Probably the reason they do that in Beast Wars, the Unicron Trilogy, Aligned etc.
I think there's an argument for igneous energon but I think that would go into Primus's blood territory and would be hard to explain off of Cybertron.
Animated's trees are just... very different. But the crystals were meant to show up so whatever.
Um, go check stuff for yourself and don't take this at face value, just like anything in the Internet. I think it's fun to try and apply real world science to fiction even if it might not make sense.