I think that this is done because the objects in the world are instanced from those primatives, this will be done for speed reasons. Other geomtry might slow it all down. I could be completely wrong, but is a best guess. Though do reply if you find a way!

I also find it incredibly difficult and honestly frustrating. I have these clear images in my head yet I lack the knowlage and familiarity with this program to bring them to life, I can't just "create" I have to really think about what I'm doing before I try just a pillar type deal and even then I still don't understand.

Yes, it's really difficult to build complexe structures with the Simplex Editor :/ But I think it was design like that because it oblige you to make simple constructions, so it doesn't slow the speed of the game due to too much objects. You also have a limit of 100 primitives per patern.
I don't think that there is a way to import your own 3D environement :/ The best things is to get used to this builder and do simple stuff, schematic figures. A good tip for that is to draw your design on paper first and to deconstruct it into big shapes, it eases the construction part in the Simplex Creator.

I don't mind building stuff from primitives, they feel like more powerful Legos. Also this way all levels still keep Race The Sun simplicity, which is one of the reasons the game works so well. I think better creativity comes from simpler tools, because designers will think more on how to work with them